Secreted salivary zsig63 polypeptide

ABSTRACT

The present invention relates to polynucleotide and polypeptide molecules for zsig63, a novel secreted salivary protein. The polypeptides, and polynucleotides encoding them, may exhibit anti-microbial activity and may be used in the study or treatment of microbial infections. The polynucleotides encoding zsig63, are located on chromosome 4, and can be used to identify a region of the genome associated with human disease states. The present invention also includes antibodies to the zsig63 polypeptides.

REFERENCE TO RELATED APPLICATIONS

This application is a Divisional of U.S. application Ser. No. 09/527,345filed Mar. 17, 2000, now U.S. Pat. No. 6,331,413 issued Dec. 18, 2001,which claims priority to U.S. Provisional Application No. 60/124,820,filed Mar. 17, 1999.

BACKGROUND OF THE INVENTION

Bacterial, and other microbial interaction with host tissues can havebeneficial (symbiotic) as well as deleterious (pathogenic) consequences.Invading microbes can be pathogenic. Consequently, host biologicaldefense strategies have evolved to protect organisms from invasion bydisease-causing microorganisms.

Microbial infection response systems include oxidative and non-oxidativemechanisms, utilizing compounds that are enzymatically synthesized incells, as well as peptides that are single gene products. For example,anti-microbial peptides constitute an oxygen-independent host defensesystem found in organisms encompassing many taxonomic families. Onemajor class of anti-microbial peptides is defined by conserved cysteineresidue patterns and is termed defensins. For example, mammaliandefensins, derived from skin, lung and intestine, exhibit antibioticactivity against a wide variety of pathogens, including Gram-positiveand Gram-negative bacteria, fungi (e.g., Candida species) and viruses.See, for example, Porter et al., Infect. Immun. 65(6): 2396-401, 1997.

A major class of microbial peptides is called adhesins. Adhesins enablemicrobes to adhere to mammalian tissues, for example the oral,gastrointestinal, urogenital and respiratory tracts. For a pathogenicmicroorganism, this may be a primary route to colonization and/orinvasion of the host. Conversely, natural microbial flora can adhere tohost tissues and create beneficial symbiotic relationships such asnutritional benefits, and protection against colonization of pathogenicmicrobes. The host defenses involved in attracting and establishingbeneficial microbial colonization, as opposed to pathogenic microbialcolonization, are not well understood. However, host defenses thataffect this balance may have anti-microbial, immunomodulatory,inflammatory, anti-inflammatory or other properties.

Thus, moieties having anti-microbial, adhesin-like, immunomodulatory,inflammatory, anti-inflammatory or other properties are sought. Thepresent invention provides such polypeptides for these and other usesthat should be apparent to those skilled in the art from the teachingsherein.

SUMMARY OF THE INVENTION

Within one aspect, the present invention provides an isolatedpolynucleotide encoding a zsig63 polypeptide comprising a sequence ofamino acid residues that is at least 90% identical to an amino acidsequence selected from the group consisting of: (a) the amino acidsequence as shown in SEQ ID NO:2 from amino acid number 16 (Arg) toamino acid number 37 (Ser); (b) the amino acid sequence as shown in SEQID NO:2 from amino acid number 38 (Leu) to amino acid number 126 (Ala);(c) the amino acid sequence as shown in SEQ ID NO:2 from amino acidnumber 127 (Pro) to amino acid number 219 (Gln); (d) the amino acidsequence as shown in SEQ ID NO:2 from amino acid number 16 (Arg) toamino acid number 219 (Gln); and (e) the amino acid sequence as shown inSEQ ID NO:2 from amino acid number 1 (Met) to amino acid number 219(Gln). In one embodiment, the isolated polynucleotide disclosed aboveencodes a zsig63 polypeptide comprising a sequence of amino acidresidues selected from the group consisting of: (a) the amino acidsequence as shown in SEQ ID NO:2 from amino acid number 16 (Arg) toamino acid number 37 (Ser); (b) the amino acid sequence as shown in SEQID NO:2 from amino acid number 38 (Leu) to amino acid number 126 (Ala);(c) the amino acid sequence as shown in SEQ ID NO: 2 from amino acidnumber 127 (Pro) to amino acid number 219 (Gln); (d) the amino acidsequence as shown in SEQ ID NO:2 from amino acid number 16 (Arg) toamino acid number 219 (Gln); and (e) the amino acid sequence as shown inSEQ ID NO:2 from amino acid number 1 (Met) to amino acid number 219(Gln). In another embodiment, the isolated polynucleotide disclosedabove is selected from the group consisting of: (a) a polynucleotidesequence as shown in SEQ ID NO:1 from nucleotide 173 to nucleotide 784;(b) a polynucleotide sequence as shown in SEQ ID NO:1 from nucleotide128 to nucleotide 784; and (c) a polynucleotide sequence complementaryto (a) or (b). In another embodiment, the isolated polynucleotidedisclosed above comprises nucleotide 1 to nucleotide 657 of SEQ ID NO:3.

Within another aspect, the present invention provides an expressionvector comprising the following operably linked elements: atranscription promoter; a DNA segment encoding a zsig63 polypeptidecomprising an amino acid sequence that is at least 90% identical to theamino acid sequence shown in SEQ ID NO:2 from amino acid number 16 (Arg)to amino acid number 219 (Gln); and a transcription terminator. In oneembodiment, the expression vector disclosed above further comprises asecretory signal sequence operably linked to the DNA segment.

Within another aspect, the present invention provides a cultured cellinto which has been introduced an expression vector as disclosed above,wherein the cell expresses a polypeptide encoded by the DNA segment.

Within another aspect, the present invention provides a DNA constructencoding a fusion protein, the DNA construct comprising: a first DNAsegment encoding a polypeptide selected from the group consisting of:(a) the amino acid sequence of SEQ ID NO:2 from residue number 1 (Met)to residue number 15 (Ala); (b) the amino acid sequence of SEQ ID NO:2from residue number 16 (Arg) to residue number 37 (Ser); (c) the aminoacid sequence of SEQ ID NO:2 from residue number 38 (Leu) to residuenumber 126 (Ala); (d) the amino acid sequence of SEQ ID NO:2 fromresidue number 127 (Pro) to residue number 219 (Gln); and (e) the aminoacid sequence of SEQ ID NO:2 from residue number 16 (Arg) to residuenumber 219 (Gln); and at least one other DNA segment encoding anadditional polypeptide, wherein the first and other DNA segments areconnected in-frame; and encode the fusion protein.

Within another aspect, the present invention provides a fusion proteinproduced by a method comprising: culturing a host cell into which hasbeen introduced a vector comprising the following operably linkedelements: (a) a transcriptional promoter; (b) a DNA construct encoding afusion protein as disclosed above; and(c) a transcriptional terminator;and recovering the protein encoded by the DNA segment.

Within another aspect, the present invention provides an isolated zsig63polypeptide comprising a sequence of amino acid residues that is atleast 90% identical to an amino acid sequence selected from the groupconsisting of: (a) the amino acid sequence as shown in SEQ ID NO:2 fromamino acid number 16 (Arg) to amino acid number 37 (Ser); (b) the aminoacid sequence as shown in SEQ ID NO:2 from amino acid number 38 (Leu) toamino acid number 126 (Ala); (c) the amino acid sequence as shown in SEQID NO:2 from amino acid number 127 (Pro) to amino acid number 219 (Gln);(d) the amino acid sequence as shown in SEQ ID NO:2 from amino acidnumber 16 (Arg) to amino acid number 219 (Gln); and (e) the amino acidsequence as shown in SEQ ID NO:2 from amino acid number 1 (Met) to aminoacid number 219 (Gln). In one embodiment, the isolated polypeptidedisclosed above comprises a sequence of amino acid residues selectedfrom the group consisting of: (a) the amino acid sequence as shown inSEQ ID NO:2 from amino acid number 16 (Arg) to amino acid number 37(Ser); (b) the amino acid sequence as shown in SEQ ID NO:2 from aminoacid number 38 (Leu) to amino acid number 126 (Ala); (c) the amino acidsequence as shown in SEQ ID NO:2 from amino acid number 127 (Pro) toamino acid number 219 (Gln); (d) the amino acid sequence as shown in SEQID NO:2 from amino acid number 16 (Arg) to amino acid number 219 (Gln);and (e) the amino acid sequence as shown in SEQ ID NO:2 from amino acidnumber 1 (Met) to amino acid number 219 (Gln).

Within another aspect, the present invention provides a method ofproducing a zsig63 polypeptide comprising: culturing a cell as disclosedabove; and isolating the zsig63 polypeptide produced by the cell.

Within another aspect, the present invention provides a method ofdetecting, in a test sample, the presence of an antagonist of zsig63protein activity, comprising: transfecting a zsig63-responsive cell,with a reporter gene construct that is responsive to a zsig63-stimulatedcellular pathway; and producing a zsig63 polypeptide by the method asdisclosed above; and adding the zsig63 polypeptide to the cell, in thepresence and absence of a test sample; and comparing levels of responseto the zsig63 polypeptide, in the presence and absence of the testsample, by a biological or biochemical assay; and determining from thecomparison, the presence of the antagonist of zsig63 activity in thetest sample.

Within another aspect, the present invention provides a method ofdetecting, in a test sample, the presence of an agonist of zsig63protein activity, comprising: transfecting a zsig63-responsive cell,with a reporter gene construct that is responsive to a zsig63-stimulatedcellular pathway; and adding a test sample; and comparing levels ofresponse in the presence and absence of the test sample, by a biologicalor biochemical assay; and determining from the comparison, the presenceof the agonist of zsig63 activity in the test sample.

Within another aspect, the present invention provides a method ofproducing an antibody to zsig63 polypeptide comprising the followingsteps in order: inoculating an animal with a polypeptide selected fromthe group consisting of: (a) a polypeptide consisting of 9 to 204 aminoacids, wherein the polypeptide consists of a contiguous sequence ofamino acids in SEQ ID NO:2 from amino acid number 16 (Ala) to amino acidnumber 219 (Gln); and (b) a polypeptide according as disclosed above;(c) a polypeptide comprising amino acid number 16 (Arg) to 37 (Ser) ofSEQ ID NO:2; (d) a polypeptide comprising amino acid number 38 (Leu) to126 (Ala) of SEQ ID NO:2; (e) a polypeptide comprising amino acid number127 (Pro) to 219 (Gln) of SEQ ID NO:2; (f) a polypeptide comprisingamino acid number 16 (Arg) to amino acid number 219 (Gln) of SEQ IDNO:2; (g) a polypeptide comprising amino acid number 1 (Met) to aminoacid number 219 (Gln) of SEQ ID NO:2; (h) a polypeptide comprising aminoacid number 14 (Phe) to 19 (Arg) of SEQ ID NO:2; (i) a polypeptidecomprising amino acid number 16 (Arg) to 21 (Phe) of SEQ ID NO:2; (j) apolypeptide comprising amino acid number 24 (Gly) to 29 (Asp) of SEQ IDNO:2; (k) a polypeptide comprising amino acid number 25 (Glu) to 30(Asp) of SEQ ID NO:2; (l) a polypeptide comprising amino acid number187Glu) to 192 (Glu) of SEQ ID NO:2; (m) a polypeptide comprising aminoacid number 24 (Gly) to 33 (Pro) of SEQ ID NO:2; (n) a polypeptidecomprising amino acid number 17 (Lys) to 33 (Pro) of SEQ ID NO:2; (o) apolypeptide comprising amino acid number 66 (Thr) to 73 (Pro) of SEQ IDNO:2; (p) a polypeptide comprising amino acid number 103 (Pro) to 108(Gly) of SEQ ID NO:2; (q) a polypeptide comprising amino acid number 190(Ala) to 197 (Glu) of SEQ ID NO:2; (r) a polypeptide comprising aminoacid number 202 (Lys ) to 215 (Gly) of SEQ ID NO:2; and (s) apolypeptide comprising amino acid number 190 (Ala) to 215 (Glu) of SEQID NO:2; and wherein the polypeptide elicits an immune response in theanimal to produce the antibody; and isolating the antibody from theanimal.

Within another aspect, the present invention provides an antibodyproduced by the method as disclosed above, which binds to a zsig63polypeptide. In one embodiment, the antibody disclosed above theantibody is a monoclonal antibody. Within another aspect, the presentinvention provides an antibody that binds to a polypeptide as disclosedabove.

These and other aspects of the invention will become evident uponreference to the following detailed description of the invention.

DETAILED DESCRIPTION OF THE INVENTION

Prior to setting forth the invention in detail, it may be helpful to theunderstanding thereof to define the following terms.

The term “affinity tag” is used herein to denote a peptide segment thatcan be attached to a polypeptide to provide for purification of thepolypeptide or provide sites for attachment of the polypeptide to asubstrate. In principal, any peptide or protein for which an antibody orother specific binding agent is available can be used as an affinitytag. Affinity tags include a poly-histidine tract, protein A (Nilsson etal., EMBO J. 4:1075, 1985; Nilsson et al., Methods Enzymol. 198:3,1991), glutathione S transferase (Smith and Johnson, Gene 67:31, 1988),substance P, Flag™ peptide (Hopp et al., Biotechnology 6:1204-1210,1988; available from Eastman Kodak Co., New Haven, Conn.), streptavidinbinding peptide, or other antigenic epitope or binding domain. See, ingeneral Ford et al., Protein Expression and Purification 2: 95-107,1991. DNAs encoding affinity tags are available from commercialsuppliers (e.g., Pharmacia Biotech, Piscataway, N.J.).

The term “allelic variant” denotes any of two or more alternative formsof a gene occupying the same chromosomal locus. Allelic variation arisesnaturally through mutation, and may result in phenotypic polymorphismwithin populations. Gene mutations can be silent (no change in theencoded polypeptide) or may encode polypeptides having altered aminoacid sequence. The term allelic variant is also used herein to denote aprotein encoded by an allelic variant of a gene.

The terms “amino-terminal” and “carboxyl-terminal” are used herein todenote positions within polypeptides and proteins. Where the contextallows, these terms are used with reference to a particular sequence orportion of a polypeptide or protein to denote proximity or relativeposition. For example, a certain sequence positioned carboxyl-terminalto a reference sequence within a protein is located proximal to thecarboxyl terminus of the reference sequence, but is not necessarily atthe carboxyl terminus of the complete protein.

The term “complement/anti-complement pair” denotes non-identicalmoieties that form a non-covalently associated, stable pair underappropriate conditions. For instance, biotin and avidin (orstreptavidin) are prototypical members of a complement/anti-complementpair. Other exemplary complement/anti-complement pairs includereceptor/ligand pairs, antibody/antigen (or hapten or epitope) pairs,sense/antisense polynucleotide pairs, and the like. Where subsequentdissociation of the complement/anti-complement pair is desirable, thecomplement/anti-complement pair preferably has a binding affinity of<10⁹ M⁻¹.

The term “complements of polynucleotide molecules” denotespolynucleotide molecules having a complementary base sequence andreverse orientation as compared to a reference -sequence. For example,the sequence 5′ATGCACGGG 3′ is complementary to 5′-CCCGTGCAT 3′.

The term “contig” denotes a polynucleotide that has a contiguous stretchof identical or complementary sequence to another polynucleotide.Contiguous sequences are said to “overlap” a given stretch ofpolynucleotide sequence either in their entirety or along a partialstretch of the polynucleotide. For example, representative contigs tothe polynucleotide sequence 5′-ATGGAGCTT-3′ are 5′-AGCTTgagt-3′ and3′-tcgacTACC-5′.

The term “degenerate nucleotide sequence” denotes a sequence ofnucleotides that includes one or more degenerate codons (as compared toa reference polynucleotide molecule that encodes a polypeptide).Degenerate codons contain different triplets of nucleotides, but encodethe same amino acid residue (i.e., GAU and GAC triplets each encodeAsp).

The term “expression vector” denotes a DNA molecule, linear or circular,that comprises a segment encoding a polypeptide of interest operablylinked to additional segments that provide for its transcription. Suchadditional segments may include promoter and terminator sequences, andmay optionally include one or more origins of replication, one or moreselectable markers, an enhancer, a polyadenylation signal, and the like.Expression vectors are generally derived from plasmid or viral DNA, ormay contain elements of both.

The term “isolated”, when applied to a polynucleotide molecule, denotesthat the polynucleotide has been removed from its natural genetic milieuand is thus free of other extraneous or unwanted coding sequences, andis in a form suitable for use within genetically engineered proteinproduction systems. Such isolated molecules are those that are separatedfrom their natural environment and include cDNA and genomic clones.Isolated DNA molecules of the present invention are free of other geneswith which they are ordinarily associated, but may include naturallyoccurring 5′ and 3′ untranslated regions such as promoters andterminators. The identification of associated regions will be evident toone of ordinary skill in the art (see for example, Dynan and Tijan,Nature 316:774-78, 1985). When applied to a protein, the term “isolated”indicates that the protein is found in a condition other than its nativeenvironment, such as apart from blood and animal tissue. In a preferredform, the isolated protein is substantially free of other proteins,particularly other proteins of animal origin. It is preferred to providethe protein in a highly purified form, i.e., greater than 95% pure, morepreferably greater than 99% pure.

The term “operably linked”, when referring to DNA segments, denotes thatthe segments are arranged so that they function in concert for theirintended purposes, e.g. transcription initiates in the promoter andproceeds through the coding segment to the terminator.

The term “ortholog” denotes a polypeptide or protein obtained from onespecies that is the functional counterpart of a polypeptide or proteinfrom a different species. Sequence differences among orthologs are theresult of speciation.

“Paralogs” are distinct but structurally related proteins made by anorganism. Paralogs are believed to arise through gene duplication. Forexample, α-globin, β-globin, and myoglobin are paralogs of each other

The term “polynucleotide” denotes a single- or double-stranded polymerof deoxyribonucleotide or ribonucleotide bases read from the 5′ to the3′ end. Polynucleotides include RNA and DNA, and may be isolated fromnatural sources, synthesized in vitro, or prepared from a combination ofnatural and synthetic molecules. Sizes of polynucleotides are expressedas base pairs (abbreviated “bp”), nucleotides (“nt”), or kilobases(“kb”). Where the context allows, the latter two terms may describepolynucleotides that are single-stranded or double-stranded. When theterm is applied to double-stranded molecules it is used to denoteoverall length and will be understood to be equivalent to the term “basepairs”. It will be recognized by those skilled in the art that the twostrands of a double-stranded polynucleotide may differ slightly inlength and that the ends thereof may be staggered as a result ofenzymatic cleavage; thus all nucleotides within a double-strandedpolynucleotide molecule may not be paired.

A “polypeptide” is a polymer of amino acid residues joined by peptidebonds, whether produced naturally or synthetically. Polypeptides of lessthan about 10 amino acid residues are commonly referred to as“peptides”.

The term “promoter” denotes a portion of a gene containing DNA sequencesthat provide for the binding of RNA polymerase and initiation oftranscription. Promoter sequences are commonly, but not always, found inthe 5′ non-coding regions of genes.

The term “receptor” denotes a cell-associated protein that binds to abioactive molecule (i.e., a ligand) and mediates the effect of theligand on the cell. Membrane-bound receptors are characterized by amulti-domain structure comprising an extracellular ligand-binding domainand an intracellular effector domain that is typically involved insignal transduction. Binding of ligand to receptor results in aconformational change in the receptor that causes an interaction betweenthe effector domain and other molecule(s) in the cell. This interactionin turn leads to an alteration in the metabolism of the cell. Metabolicevents that are linked to receptor-ligand interactions include genetranscription, phosphorylation, dephosphorylation, increases in cyclicAMP production, mobilization of cellular calcium, mobilization ofmembrane lipids, cell adhesion, hydrolysis of inositol lipids andhydrolysis of phospholipids. Most nuclear receptors also exhibit amulti-domain structure, including an amino-terminal, transactivatingdomain, a DNA binding domain and a ligand-binding domain. In general,receptors can be membrane bound, cytosolic or nuclear; monomeric (e.g.,thyroid stimulating hormone receptor, beta-adrenergic receptor) ormultimeric (e.g., PDGF receptor, growth hormone receptor, IL-3 receptor,GM-CSF receptor, G-CSF receptor, erythropoietin receptor and IL-6receptor).

The term “secretory signal sequence” denotes a DNA sequence that encodesa polypeptide (a “secretory peptide”) that, as a component of a largerpolypeptide, directs the larger polypeptide through a secretory pathwayof a cell in which it is synthesized. The larger peptide is commonlycleaved to remove the secretory peptide during transit through thesecretory pathway.

A “soluble receptor” is a receptor polypeptide that is not bound to acell membrane. Soluble receptors are most commonly ligand-bindingreceptor polypeptides that lack transmembrane and cytoplasmic domains.Soluble receptors can comprise additional amino acid residues, such asaffinity tags that provide for purification of the polypeptide orprovide sites for attachment of the polypeptide to a substrate, orimmunoglobulin constant region sequences. Many cell-surface receptorshave naturally occurring, soluble counterparts that are produced byproteolysis or translated from alternatively spliced mRNAs. Receptorpolypeptides are said to be substantially free of transmembrane andintracellular polypeptide segments when they lack sufficient portions ofthese segments to provide membrane anchoring or signal transduction,respectively.

Molecular weights and lengths of polymers determined by impreciseanalytical methods (e.g., gel electrophoresis) will be understood to beapproximate values. When such a value is expressed as “about” X or“approximately” X, the stated value of X will be understood to beaccurate to ±10%.

All references cited herein are incorporated by reference in theirentirety.

The present invention is based in part upon the discovery of a novel DNAsequence that encodes a human polypeptide having structural similarityto proteins of the bacterial adhesin family.

A standard Northern blot tissue distribution of the mRNA correspondingto this novel DNA revealed high expression in salivary gland, andmoderate to high expression in thyroid. Such high expression in salivarygland is consistent with the knowledge in the art regardinganti-bacterial polypeptides, such as defensins, i.e., that they areexpressed in epithelial tissues, and are highly inducible upon microbialinfection.

The novel zsig63 polypeptides of the present invention were initiallyidentified by querying an EST database for proteins homologous toproteins having a secretory signal sequence. These proteins arecharacterized by an upstream methionine start site and a hydrophobicregion of approximately 13 amino acids, followed by a peptide signalpeptidase cleavage site. An EST database was queried for novel DNAsequences whose translations would meet these search criteria. An ESTwas found and its corresponding cDNA was sequenced. The zsig63nucleotide sequence is believed to encode the entire coding sequence ofthe predicted protein. Zsig63 may be a novel host-defense polypeptide,immune modulating factor, anti-pathogenic polypeptide, cell-cellsignaling molecule, growth factor, cytokine, secreted extracellularmatrix associated protein with growth factor hormone activity, or thelike, and is a member a novel protein family.

The sequence of the zsig63 polypeptide was obtained from a single clonebelieved to contain its corresponding polynucleotide sequence. The clonewas obtained from a salivary gland library. Other libraries that mightalso be searched for such sequences include thyroid, prostate, and thelike.

The nucleotide sequence of a representative zsig63-encoding DNA isdescribed in SEQ ID NO:1 (from nucleotide 128 to 784), and its deduced219 amino acid sequence is described in SEQ ID NO:2. In its entirety,the zsig63 polypeptide (SEQ ID NO:2) represents a full-lengthpolypeptide segment (residue 1 (Met) to residue 219 (Gln) of SEQ IDNO:2). The domains and structural features of the zsig63 polypeptide arefurther described below.

Analysis of the zsig63 polypeptide encoded by the DNA sequence of SEQ IDNO:1 revealed an open reading frame encoding 219 amino acids (SEQ IDNO:2) comprising a predicted secretory signal peptide of 15 amino acidresidues (residue 1 (Met) to residue 15 (Ala) of SEQ ID NO:2), and amature polypeptide of 204 amino acids (residue 16 (Arg) to residue 219(Gln) of SEQ ID NO:2). Structural analysis revealed the following 3structural domains:

(1) The first domain, referred to hereinafter as “domain 1,” correspondsapproximately to amino acid residues 16 (Arg) to amino acid residue 37(Ser) of SEQ ID NO:2. Domain 1 contains an acid region of 5 acidresidues (corresponding to amino acid residues 25 (Glu) to amino acidresidue 30 (Asp) of SEQ ID NO:2).

(2) The second domain, referred to hereinafter as “domain 2,”corresponds approximately to amino acid residues 38 (Leu) to amino acidresidue 126 (Ala) of SEQ ID NO:2. Domain 2 contains a high concentrationof Tyrosine residues (16% over 49 amino acids). Tyrosine residues indomain 2 are present, in reference to SEQ ID NO:2 at the followingpositions: 42, 52, 53, 62, 67, 75, 86, and 88.

(3) The third domain, referred to hereinafter as “domain 3,” correspondsapproximately to amino acid residues 127 (Pro) to amino acid residue 219(Gln) of SEQ ID NO:2. Domain 3 contains a region rich in coil-likestructure (corresponding to amino acid residues 127 (Pro) to amino acidresidue 208 (Pro) of SEQ ID NO:2) that contains 16 full evenly-spacedcoil-like repeats punctuated by proline residues every 5 amino acids.These repeats are defined as follows, based on the proline residues andcorresponding reference to SEQ ID NO:2:

“repeat 1” corresponding to amino acid residues 124 (Ile) to amino acidresidue 133 (Pro) of SEQ ID NO:2;

“repeat 2” corresponding to amino acid residues 134 (Ala) to amino acidresidue 138 (Pro) of SEQ ID NO:2;

“repeat 3” corresponding to amino acid residues 139 (Leu) to amino acidresidue 143 (Pro) of SEQ ID NO:2;

“repeat 4” corresponding to amino acid residues 144 (Val) to amino acidresidue 148 (Pro) of SEQ ID NO:2;

“repeat 5” corresponding to amino acid residues 149 (Ala) to amino acidresidue 153 (Pro) of SEQ ID NO:2;

“repeat 6” corresponding to amino acid residues 154 (Val) to amino acidresidue 158 (Pro) of SEQ ID NO:2.

“repeat 7” corresponding to amino acid residues 159 (Ala) to amino acidresidue 163 (Pro) of SEQ ID NO:2;

“repeat 8” corresponding to amino acid residues 164 (Val) to amino acidresidue 168 (Pro) of SEQ ID NO:2;

“repeat 9” corresponding to amino acid residues 169 (Ala) to amino acidresidue 173 (Pro) of SEQ ID NO:2;

“repeat 10” corresponding to amino acid residues 174 (Val) to amino acidresidue 178 (Pro) of SEQ ID NO:2;

“repeat 11” corresponding to amino acid residues 179 (Ala) to amino acidresidue 183 (Pro) of SEQ ID NO:2;

“repeat 12” corresponding to amino acid residues 184 (Val) to amino acidresidue 188 (Pro) of SEQ ID NO:2.

“repeat 13” corresponding to amino acid residues 189 (Ala) to amino acidresidue 193 (Pro) of SEQ ID NO:2;

“repeat 14” corresponding to amino acid residues 194 (Ser) to amino acidresidue 198 (Pro) of SEQ ID NO:2;

“repeat 15” corresponding to amino acid residues 199 (Ala) to amino acidresidue 203 (Pro) of SEQ ID NO:2; and

“repeat 16” corresponding to amino acid residues 204 (Ala) to amino acidresidue 208 (Pro) of SEQ ID NO:2.

Structural modeling is performed by one of skill in the art, usingmodelling software, such as InsightII® (Biosym/MSI, San Diego, Calif.).The presence of low variance and structural motifs generally correlatewith or define important structural regions in proteins. Regions of lowvariance (e.g., hydrophobic clusters) are generally present in regionsof structural importance (Sheppard, P. et al., supra.). Such regions oflow variance often contain rare or infrequent amino acids, such asTryptophan. The regions flanking and between such conserved and lowvariance motifs may be more variable, but are often functionallysignificant because they may relate to or define important structuresand activities such as binding domains, biological and enzymaticactivity, signal transduction, cell-cell interaction, tissuelocalization domains and the like.

The coil-like repeats in domain 3 of zsig63 polypeptide can be used as atool to identify new family members. For instance, reversetranscription-polymerase chain reaction (RT-PCR) can be used to amplifysequences encoding the conserved motif from RNA obtained from a varietyof tissue sources. More specifically, degenerate DNA probes anddegenerate primers can be employed to identify other human orzsig63-like polynucleotides. In particular, highly degenerate primersdesigned from the above sequences are useful for this purpose.

SEQ ID NO:3 is a degenerate polynucleotide sequence that encompasses allpolynucleotides that encode the zsig63 polypeptide of SEQ ID NO:2. Thus,zsig63 polypeptide-encoding polynucleotides ranging from nucleotide 1 tonucleotide 657 of SEQ ID NO:3 are contemplated by the present invention.Also contemplated by the present invention are fragments and fusions asdescribed above with respect to SEQ ID NO:1 and which are formed fromanalogous regions of SEQ ID NO:3. The symbols in SEQ ID NO:3 aresummarized in Table 1 below.

TABLE 1 Nucleotide Resolutions Complement Resolutions A A T T C C G G GG C C T T A A R A|G Y C|T Y C|T R A|G M A|C K G|T K G|T M A|C S C|G SA|T W A|T W C|G H A|C|T D A|G|T B C|G|T V A|C|G V A|C|G B C|G|T D A|G|TH A|C|T N A|C|G|T N A|C|G|T

The degenerate codons used in SEQ ID NO:3 encompass all possible codonsfor a given amino acid, are set forth in Table 2 below.

TABLE 2 Amino Degenerate Acid Letter Codons Codon Cys C TGC TGT TGY SerS AGC AGT TCA TCC TCG TCT WSN Thr T ACA ACC ACG ACT ACN Pro P CCA CCCCCG CCT CCN Ala A GCA GCC GCG GCT GCN Gly G GGA GGC GGG GGT GGN Asn NAAC AAT AAY Asp D GAC GAT GAY Glu E GAA GAG GAR Gln Q CAA CAG CAR His HCAC CAT CAY Arg R AGA AGG CGA CGC CGG CGT MGN Lys K AAA AAG AAR Met MATG ATG Ile I ATA ATC ATT ATH Leu L CTA CTC CTG CTT TTA TTG YTN Val VGTA GTC GTG GTT GTN Phe F TTC TTT TTY Tyr Y TAC TAT TAY Trp W TGG TGGTer . TAA TAG TGA TRR Asn|Asp B RAY Glu|Gln Z SAR Any X NNN Gap — —

One of ordinary skill in the art will appreciate that some ambiguity isintroduced in determining a degenerate codon, representative of allpossible codons encoding each amino acid. For example, the degeneratecodon for serine (WSN) can, in some circumstances, encode arginine(AGR), and the degenerate codon for arginine (MGN) can, in somecircumstances, encode serine (AGY). A similar relationship existsbetween codons encoding phenylalanine and leucine. Thus, somepolynucleotides encompassed by the degenerate sequence may encodevariant amino acid sequences, but one of ordinary skill in the art caneasily identify such variant sequences by reference to the amino acidsequence of SEQ ID NO:2. Variant sequences can be readily tested forfunctionality as described herein.

One of ordinary skill in the art will also appreciate that differentspecies can exhibit “preferential codon usage.” In general, see,Grantham, et al., Nuc. Acids Res. 8:1893-912, 1980; Haas, et al. Curr.Biol. 6:315-24, 1996; Wain-Hobson, et al., Gene 13:355-64, 1981;Grosjean and Fiers, Gene 18:199-209, 1982; Holm, Nuc. Acids Res.14:3075-87, 1986; Ikemura, J. Mol. Biol. 158:573-97, 1982. As usedherein, the term “preferential codon usage” or “preferential codons” isa term of art referring to protein translation codons that are mostfrequently used in cells of a certain species, thus favoring one or afew representatives of the possible codons encoding each amino acid (SeeTable 2). For example, the amino acid Threonine (Thr) may be encoded byACA, ACC, ACG, or ACT, but in mammalian cells ACC is the most commonlyused codon; in other species, for example, insect cells, yeast, virusesor bacteria, different Thr codons may be preferential. Preferentialcodons for a particular species can be introduced into thepolynucleotides of the present invention by a variety of methods knownin the art. Introduction of preferential codon sequences intorecombinant DNA can, for example, enhance production of the protein bymaking protein translation more efficient within a particular cell typeor species. Therefore, the degenerate codon sequence disclosed in SEQ IDNO:3 serves as a template for optimizing expression of polynucleotidesin various cell types and species commonly used in the art and disclosedherein. Sequences containing preferential codons can be tested andoptimized for expression in various species, and tested forfunctionality as disclosed herein.

Within preferred embodiments of the invention the isolatedpolynucleotides will hybridize to similar sized regions of SEQ ID NO:1,or a sequence complementary thereto, under stringent conditions. Ingeneral, stringent conditions are selected to be about 5° C. lower thanthe thermal melting point (T_(m)) for the specific sequence at a definedionic strength and pH. The T_(m) is the temperature (under defined ionicstrength and pH) at which 50% of the target sequence hybridizes to aperfectly matched probe. Numerous equations for calculating T_(m) areknown in the art, and are specific for DNA, RNA and DNA-RNA hybrids andpolynucleotide probe sequences of varying length (see, for example,Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition(Cold Spring Harbor Press 1989); Ausubel et al., (eds.), CurrentProtocols in Molecular Biology (John Wiley and Sons, Inc. 1987); Bergerand Kimmel (eds.), Guide to Molecular Cloning Techniques, (AcademicPress, Inc. 1987); and Wetmur, Crit. Rev. Biochem. Mol. Biol. 26:227(1990)). Sequence analysis software such as OLIGO 6.0 (LSR; Long Lake,Minn.) and Primer Premier 4.0™ (Premier Biosoft International; PaloAlto, Calif.), as well as sites on the Internet, are available tools foranalyzing a given sequence and calculating T_(m) based on user definedcriteria. Such programs can also analyze a given sequence under definedconditions and identify suitable probe sequences. Typically,hybridization of longer polynucleotide sequences, >50 base pairs, isperformed at temperatures of about 20-25° C. below the calculated T_(m).For smaller probes, <50 base pairs, hybridization is typically carriedout at the T_(m) or 5-10° C. below. This allows for the maximum rate ofhybridization for DNA-DNA and DNA-RNA hybrids. Higher degrees ofstringency at lower temperatures can be achieved with the addition offormamide which reduces the T_(m) of the hybrid about 1° C. for each 1%formamide in the buffer solution. Suitable stringent hybridizationconditions are equivalent to about a 5 h to overnight incubation atabout 42° C. in a solution comprising: about 40-50% formamide, up toabout 6×SSC, about 5×Denhardt's solution, zero up to about 10% dextransulfate, and about 10-20 μg/ml denatured commercially-available carrierDNA. Generally, such stringent conditions include temperatures of 20-70°C. and a hybridization buffer containing up to 6×SSC and 0-50%formamide; hybridization is then followed by washing filters in up toabout 2×SSC. For example, a suitable wash stringency is equivalent to0.1×SSC to 2×SSC, 0.1% SDS, at 55° C. to 65° C. Different degrees ofstringency can be used during hybridization and washing to achievemaximum specific binding to the target sequence. Typically, the washesfollowing hybridization are performed at increasing degrees ofstringency to remove non-hybridized polynucleotide probes fromhybridized complexes. Stringent hybridization and wash conditions dependon the length of the probe, reflected in the Tm, hybridization and washsolutions used, and are routinely determined empirically by one of skillin the art.

As previously noted, the isolated polynucleotides of the presentinvention include DNA and RNA. Methods for isolating DNA and RNA arewell known in the art. It is generally preferred to isolate RNA frombronchial epithelium, although DNA can also be prepared using RNA fromother tissues or isolated as genomic DNA. Total RNA can be preparedusing guanidine HCl extraction followed by isolation by centrifugationin a CsCl gradient (Chirgwin et al., Biochemistry 18:52-94, 1979). Poly(A)⁺ RNA is prepared from total RNA using the method of Aviv and Leder(Proc. Natl. Acad. Sci. USA 69:1408-1412, 1972). Complementary DNA(cDNA) is prepared from poly(A)⁺ RNA using known methods.Polynucleotides encoding zsig63 polypeptides are then identified andisolated by, for example, hybridization or PCR.

The present invention further provides counterpart polypeptides andpolynucleotides from other species (orthologs). These species include,but are not limited to mammalian, avian, amphibian, reptile, fish,insect and other vertebrate and invertebrate species. Of particularinterest are zsig63 polypeptides from other mammalian species, includingmurine, rat, porcine, ovine, bovine, canine, feline, equine and otherprimate proteins. Species homologs of the human proteins can be clonedusing information and compositions provided by the present invention incombination with conventional cloning techniques. For example, a cDNAcan be cloned using mRNA obtained from a tissue or cell type thatexpresses the protein. Suitable sources of mRNA can be identified byprobing Northern blots with probes designed from the sequences disclosedherein. A library is then prepared from mRNA of a positive tissue ofcell line. A zsig63 polypeptide-encoding cDNA can then be isolated by avariety of methods, such as by probing with a complete or partial humancDNA or with one or more sets of degenerate probes based on thedisclosed sequences. A cDNA can also be cloned using the polymerasechain reaction, or PCR (Mullis, U.S. Pat. No. 4,683,202), using primersdesigned from the sequences disclosed herein. Within an additionalmethod, the cDNA library can be used to transform or transfect hostcells, and expression of the cDNA of interest can be detected with anantibody to zsig63 polypeptide. Similar techniques can also be appliedto the isolation of genomic clones.

Those skilled in the art will recognize that the sequences disclosed inSEQ ID NO:1 and SEQ ID NO:2 represent a single allele of the humanzsig63 gene and polypeptide, and that allelic variation and alternativesplicing are expected to occur. Allelic variants can be cloned byprobing cDNA or genomic libraries from different individuals accordingto standard procedures. Allelic variants of the DNA sequence shown inSEQ ID NO:2 including those containing silent mutations and those inwhich mutations result in amino acid sequence changes, are within thescope of the present invention.

The present invention also provides isolated zsig63 polypeptides thatare substantially similar to the polypeptides of SEQ ID NO:2 and theirorthologs. The term “substantially similar” is used herein to denotepolypeptides having 60%, preferably 70% and more preferably at least80%, sequence identity to the sequences shown in SEQ ID NO:2 or theirorthologs or paralogs. Such polypeptides will more preferably be atleast 90% identical, and most preferably 95% or more identical to SEQ IDNO:2 or its orthologs or paralogs. Percent sequence identity isdetermined by conventional methods. See, for example, Altschul et al.,Bull. Math. Bio. 48: 603-616, 1986 and Henikoff and Henikoff, Proc.Natl. Acad. Sci. USA 89:10915-10919, 1992. Briefly, two amino acidsequences are aligned to optimize the alignment scores using a gapopening penalty of 10, a gap extension penalty of 1, and the “blosum 62”scoring matrix of Henikoff and Henikoff (ibid.) as shown in Table 3(amino acids are indicated by the standard one-letter codes). Thepercent identity is then calculated as:$\frac{{Total}\quad {number}\quad {of}\quad {identical}\quad {matches}}{\begin{matrix}\left\lbrack {{length}\quad {of}\quad {the}\quad {longer}\quad {sequence}\quad {plus}\quad {the}} \right. \\{{number}\quad {of}\quad {gaps}\quad {introduced}\quad {into}\quad {the}\quad {longer}} \\{{sequence}\quad {in}\quad {order}\quad {to}\quad {align}\quad {the}\quad {two}} \\\left. {sequences} \right\rbrack\end{matrix}} \times 100$

TABLE 3 A R N D C Q E G H I L K M F P S T W Y V A 4 R −1 5 N −2 0 6 D −2−2 1 6 C 0 −3 −3 −3 9 Q −1 1 0 0 −3 5 E −1 0 0 2 −4 2 5 G 0 −2 0 −1 −3−2 −2 6 H −2 0 1 −1 −3 0 0 −2 8 I −1 −3 −3 −3 −1 −3 −3 −4 −3 4 L −1 −2−3 −4 −1 −2 −3 −4 −3 2 4 K −1 2 0 −1 −3 1 1 −2 −1 −3 −2 5 M −1 −1 −2 −3−1 0 −2 −3 −2 1 2 −1 5 F −2 −3 −3 −3 −2 −3 −3 −3 −1 0 0 −3 0 6 P −1 −2−2 −1 −3 −1 −1 −2 −2 −3 −3 −1 −2 −4 7 S 1 −1 1 0 −1 0 0 0 −1 −2 −2 0 −1−2 −1 4 T 0 −1 0 −1 −1 −1 −1 −2 −2 −1 −1 −1 −1 −2 −1 1 5 W −3 −3 −4 −4−2 −2 −3 −2 −2 −3 −2 −3 −1 1 −4 −3 −2 11 Y −2 −2 −2 −3 −2 −1 −2 −3 2 −1−1 −2 −1 3 −3 −2 −2 2 7 V 0 −3 −3 −3 −1 −2 −2 −3 −3 3 1 −2 1 −1 −2 −2 0−3 −1 4

Sequence identity of polynucleotide molecules is determined by similarmethods using a ratio as disclosed above.

Those skilled in the art appreciate that there are many establishedalgorithms available to align two amino acid sequences. The “FASTA”similarity search algorithm of Pearson and Lipman is a suitable proteinalignment method for examining the level of identity shared by an aminoacid sequence disclosed herein and the amino acid sequence of a putativevariant zsig63. The FASTA algorithm is described by Pearson and Lipman,Proc. Nat'l Acad. Sci. USA 85:2444 (1988), and by Pearson, Meth.Enzymol. 183:63 (1990).

Briefly, FASTA first characterizes sequence similarity by identifyingregions shared by the query sequence (e.g., SEQ ID NO:2) and a testsequence that have either the highest density of identities (if the ktupvariable is 1) or pairs of identities (if ktup=2), without consideringconservative amino acid substitutions, insertions, or deletions. The tenregions with the highest density of identities are then rescored bycomparing the similarity of all paired amino acids using an amino acidsubstitution matrix, and the ends of the regions are “trimmed” toinclude only those residues that contribute to the highest score. Ifthere are several regions with scores greater than the “cutoff” value(calculated by a predetermined formula based upon the length of thesequence and the ktup value), then the trimmed initial regions areexamined to determine whether the regions can be joined to form anapproximate alignment with gaps. Finally, the highest scoring regions ofthe two amino acid sequences are aligned using a modification of theNeedleman-Wunsch-Sellers algorithm (Needleman and Wunsch, J. Mol. Biol.48:444 (1970); Sellers, SIAM J. Appl. Math. 26:787 (1974)), which allowsfor amino acid insertions and deletions. Illustrative parameters forFASTA analysis are: ktup=1, gap opening penalty=10, gap extensionpenalty=1, and substitution matrix=BLOSUM62. These parameters can beintroduced into a FASTA program by modifying the scoring matrix file(“SMATRIX”), as explained in Appendix 2 of Pearson, Meth. Enzymol.183:63 (1990).

FASTA can also be used to determine the sequence identity of nucleicacid molecules using a ratio as disclosed above. For nucleotide sequencecomparisons, the ktup value can range between one to six, preferablyfrom four to six.

The BLOSUM62 table (Table 3) is an amino acid substitution matrixderived from about 2,000 local multiple alignments of protein sequencesegments, representing highly conserved regions of more than 500 groupsof related proteins (Henikoff and Henikoff, Proc. Nat'l Acad. Sci. USA89:10915 (1992)). Accordingly, the BLOSUM62 substitution frequencies canbe used to define conservative amino acid substitutions that may beintroduced into the amino acid sequences of the present invention.Although it is possible to design amino acid substitutions based solelyupon chemical properties (as discussed below), the language“conservative amino acid substitution” preferably refers to asubstitution represented by a BLOSUM62 value of greater than −1. Forexample, an amino acid substitution is conservative if the substitutionis characterized by a BLOSUM62 value of 0, 1, 2, or 3. According to thissystem, preferred conservative amino acid substitutions arecharacterized by a BLOSUM62 value of at least 1 (e.g., 1, 2 or 3), whilemore preferred conservative amino acid substitutions are characterizedby a BLOSUM62 value of at least 2 (e.g., 2 or 3).

Variant proteins and polypeptides are characterized as having one ormore amino acid substitutions, deletions or additions. These changes arepreferably of a minor nature, that is conservative amino acidsubstitutions (see Table 4) and other substitutions that do notsignificantly affect the folding or activity of the protein orpolypeptide; small deletions, typically of one to about 30 amino acids;and small amino- or carboxyl-terminal extensions, such as anamino-terminal methionine residue, a small linker peptide of up to about20-25 residues, or a small extension that facilitates purification (anaffinity tag), such as a poly-histidine tract, protein A (Nilsson etal., EMBO J. 4:1075, 1985; Nilsson et al., Methods Enzymol. 198:3,1991), glutathione S transferase (Smith and Johnson, Gene 67:31, 1988),maltose binding protein (Kellerman and Ferenci, Methods Enzymol.90:459-463, 1982; Guan et al., Gene 67:21-30, 1987), thioredoxin,ubiquitin, cellulose binding protein, T7 polymerase, or other antigenicepitope or binding domain. See, in general Ford et al., ProteinExpression and Purification 2: 95-107, 1991. DNAs encoding affinity tagsare available from commercial suppliers (e.g., Pharmacia Biotech,Piscataway, N.J.; New England Biolabs, Beverly, Mass.). The presentinvention thus includes polypeptides of from about 170 to about 250amino acid residues that comprise a sequence that is at least 80%,preferably at least 90%, and more preferably 95% or more identical tothe corresponding region of SEQ ID NO:2. Polypeptides comprisingaffinity tags can further comprise a proteolytic cleavage site betweenthe zsig63 polypeptide and the affinity tag. Preferred such sitesinclude thrombin cleavage sites and factor Xa cleavage sites.

TABLE 4 Conservative amino acid substitutions Basic: arginine lysinehistidine Acidic: glutamic acid aspartic acid Polar: glutamineasparagine Hydrophobic: leucine isoleucine valine Aromatic:phenylalanine tryptophan tyrosine Small: glycine alanine serinethreonine methionine

The proteins of the present invention can also comprise, in addition tothe 20 standard amino acids, non-naturally occurring amino acidresidues. Non-naturally occurring amino acids include, withoutlimitation, trans-3-methylproline, 2,4-methanoproline,cis-4-hydroxyproline, trans-4-hydroxyproline, N-methyl-glycine,allo-threonine, methylthreonine, hydroxyethyl-cysteine,hydroxyethylhomocysteine, nitroglutamine, homoglutamine, pipecolic acid,tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenylalanine,4-azaphenyl-alanine, 4-fluorophenylalanine, 4-hydroxyproline, 6-N-methyllysine, 2-aminoisobutyric acid, isovaline and a-methyl serine. Severalmethods are known in the art for incorporating non-naturally occurringamino acid residues into proteins. For example, an in vitro system canbe employed wherein nonsense mutations are suppressed using chemicallyaminoacylated suppressor tRNAs. Methods for synthesizing amino acids andaminoacylating tRNA are known in the art. Transcription and translationof plasmids containing nonsense mutations are carried out in a cell freesystem comprising an E. coli S30 extract and commercially availableenzymes and other reagents. Proteins are purified by chromatography.See, for example, Robertson et al., J. Am. Chem. Soc. 113:2722, 1991;Ellman et al., Meth. Enzymol. 202:301, 1991; Chung et al., Science259:806-09, 1993; and Chung et al., Proc. Natl. Acad. Sci. USA90:10145-49, 1993). In a second method, translation is carried out inXenopus oocytes by microinjection of mutated mRNA and chemicallyaminoacylated suppressor tRNAs (Turcatti et al., J. Biol. Chem.271:19991-98, 1996). Within a third method, E. coli cells are culturedin the absence of a natural amino acid that is to be replaced (e.g.,phenylalanine) and in the presence of the desired non-naturallyoccurring amino acid(s) (e.g., 2-azaphenylalanine, 3-azaphenylalanine,4-azaphenylalanine, or 4-fluorophenylalanine). The non-naturallyoccurring amino acid is incorporated into the protein in place of itsnatural counterpart. See, Koide et al., Biochem. 33:7470-76, 1994.Naturally occurring amino acid residues can be converted tonon-naturally occurring species by in vitro chemical modification.Chemical modification can be combined with site-directed mutagenesis tofurther expand the range of substitutions (Wynn and Richards, ProteinSci. 2:395-403, 1993).

A limited number of non-conservative amino acids, amino acids that arenot encoded by the genetic code, non-naturally occurring amino acids,and unnatural amino acids may be substituted for zsig63 polypeptideamino acid residues. “Unnatural amino acids” have been modified afterprotein synthesis, and/or have a chemical structure in their sidechain(s) different from that of the standard amino acids. Unnaturalamino acids can be chemically synthesized, or preferably, arecommercially available, and include pipecolic acid, thiazolidinecarboxylic acid, dehydroproline, 3- and 4-methylproline, and3,3-dimethylproline.

Essential amino acids in the zsig63 polypeptides of the presentinvention can be identified according to procedures known in the art,such as site-directed mutagenesis or alanine-scanning mutagenesis(Cunningham and Wells, Science 244: 1081-1085, 1989). In the lattertechnique, single alanine mutations are introduced at every residue inthe molecule, and the resultant mutant molecules are tested forbiological activity (e.g., anti-microbial activity) to identify aminoacid residues that are critical to the activity of the molecule. Seealso, Hilton et al., J. Biol. Chem. 271:4699-4708, 1996. Sites ofligand-receptor or other biological interaction can also be determinedby physical analysis of structure, as determined by such techniques asnuclear magnetic resonance, crystallography, electron diffraction orphotoaffinity labeling, in conjunction with mutation of putative contactsite amino acids. See, for example, de Vos et al., Science 255:306-312,1992; Smith et al., J. Mol. Biol. 224:899-904, 1992; Wlodaver et al.,FEBS Lett. 309:59-64, 1992. The identities of essential amino acids canalso be inferred from analysis of homologies with related β-defensins.

Determination of amino acid residues that are within regions or domainsthat are critical to maintaining structural integrity can be determined.Within these regions one can determine specific residues that will bemore or less tolerant of change and maintain the overall tertiarystructure of the molecule. Methods for analyzing sequence structureinclude, but are not limited to, alignment of multiple sequences withhigh amino acid or nucleotide identity and computer analysis usingavailable software (e.g., the Insight II® viewer and homology modelingtools; MSI, San Diego, Calif.), secondary structure propensities, binarypatterns, complementary packing and buried polar interactions (Barton,Current Opin. Struct. Biol. 5:372-376, 1995 and Cordes et al., CurrentOpin. Struct. Biol. 6:3-10, 1996). In general, when designingmodifications to molecules or identifying specific fragmentsdetermination of structure will be accompanied by evaluating activity ofmodified molecules.

Amino acid sequence changes are made in zsig63 polypeptides so as tominimize disruption of higher order structure essential to biologicalactivity. For example, when the zsig63 polypeptide comprises one or morehelices, changes in amino acid residues will be made so as not todisrupt the helix geometry and other components of the molecule wherechanges in conformation abate some critical function, for example,binding of the molecule to its binding partners. The effects of aminoacid sequence changes can be predicted by, for example, computermodeling as disclosed above or determined by analysis of crystalstructure (see, e.g., Lapthom et al., Nat. Struct. Biol. 2:266-268,1995). Other techniques that are well known in the art compare foldingof a variant protein to a standard molecule (e.g., the native protein).For example, comparison of the cysteine pattern in a variant andstandard molecules can be made. Mass spectrometry and chemicalmodification using reduction and alkylation provide methods fordetermining cysteine residues which are associated with disulfide bondsor are free of such associations (Bean et al., Anal. Biochem.201:216-226, 1992; Gray, Protein Sci. 2:1732-1748, 1993; and Pattersonet al., Anal. Chem. 66:3727-3732, 1994). It is generally believed thatif a modified molecule does not have the same disulfide bonding patternas the standard molecule folding would be affected. Another well knownand accepted method for measuring folding is circular dichrosism (CD).Measuring and comparing the CD spectra generated by a modified moleculeand standard molecule is routine (Johnson, Proteins 7:205-214, 1990).Crystallography is another well known method for analyzing folding andstructure. Nuclear magnetic resonance (NMR), digestive peptide mappingand epitope mapping are also known methods for analyzing folding andstructural similarities between proteins and polypeptides (Schaanan etal., Science 257:961-964, 1992).

A Hopp/Woods hydrophilicity profile of the zsig63 protein sequence asshown in SEQ ID NO:2 can be generated (Hopp et al., Proc. Natl. Acad.Sci.78:3824-3828, 1981; Hopp, J. Immun. Meth. 88:1-18, 1986 and Triquieret al., Protein Engineering 11:153-169, 1998). The profile is based on asliding six-residue window. Buried G, S, and T residues and exposed H,Y, and W residues were ignored. For example, in zsig63, hydrophilicregions include amino acid residues 14 (Phe) to 19 (Arg) of SEQ ID NO:2,amino acid residues 16 (Arg) to 21 (Phe) of SEQ ID NO:2, amino acidresidues 24 (Gly) to 29 (Asp) of SEQ ID NO:2, amino acid residues 25(Glu) to 30 (Asp) of SEQ ID NO:2, and amino acid residues 187Glu) to 192(Glu) of SEQ ID NO:2.

Those skilled in the art will recognize that hydrophilicity orhydrophobicity will be taken into account when designing modificationsin the amino acid sequence of a zsig63 polypeptide, so as not to disruptthe overall structural and biological profile. Of particular interestfor replacement are hydrophobic residues selected from the groupconsisting of Val, Leu and Ile or the group consisting of Met, Gly, Ser,Ala, Tyr and Trp. For example, residues tolerant of substitution couldinclude such residues as shown in SEQ ID NO:2., and described above.

The identities of essential amino acids can also be inferred fromanalysis of sequence similarity between other known zsig63 proteinfamily members with zsig63. Using methods such as “FASTA” analysisdescribed previously, regions of high similarity are identified within afamily of proteins and used to analyze amino acid sequence for conservedregions. An alternative approach to identifying a variant zsig63polynucleotide on the basis of structure is to determine whether anucleic acid molecule encoding a potential variant zsig63 polynucleotidecan hybridize to a nucleic acid molecule having the nucleotide sequenceof SEQ ID NO:1, as discussed above.

Other methods of identifying essential amino acids in the polypeptidesof the present invention are procedures known in the art, such assite-directed mutagenesis or alanine-scanning mutagenesis (Cunninghamand Wells, Science 244:1081 (1989), Bass et al., Proc. Natl Acad. Sci.USA 88:4498 (1991), Coombs and Corey, “Site-Directed Mutagenesis andProtein Engineering,” in Proteins: Analysis and Design, Angeletti (ed.),pages 259-311 (Academic Press, Inc. 1998)). In the latter technique,single alanine mutations are introduced at every residue in themolecule, and the resultant mutant molecules are tested for biologicalactivity as disclosed below to identify amino acid residues that arecritical to the activity of the molecule. See also, Hilton et al., J.Biol. Chem. 271:4699 (1996).

The present invention also includes functional fragments of zsig63polypeptides and nucleic acid molecules encoding such functionalfragments. A “functional” zsig63 or fragment thereof defined herein ischaracterized by its proliferative or differentiating activity, by itsability to induce or inhibit specialized cell functions, or by itsability to bind specifically to an anti-zsig63 antibody or zsig63receptor (either soluble or immobilized).

Routine deletion analyses of nucleic acid molecules can be performed toobtain functional fragments of a nucleic acid molecule that encodes azsig63 polypeptide. As an illustration, DNA molecules having thenucleotide sequence of SEQ ID NO:1 or fragments thereof, can be digestedwith Bal31 nuclease to obtain a series of nested deletions. These DNAfragments are then inserted into expression vectors in proper readingframe, and the expressed polypeptides are isolated and tested for zsig63activity, or for the ability to bind anti-zsig63 antibodies or zsig63receptor. One alternative to exonuclease digestion is to useoligonucleotide-directed mutagenesis to introduce deletions or stopcodons to specify production of a desired zsig63 fragment.Alternatively, particular fragments of a zsig63 polynucleotide can besynthesized using the polymerase chain reaction.

Standard methods for identifying functional domains are well-known tothose of skill in the art. For example, studies on the truncation ateither or both termini of interferons have been summarized byHorisberger and Di Marco, Pharmac. Ther. 66:507 (1995). Moreover,standard techniques for functional analysis of proteins are describedby, for example, Treuter et al., Molec. Gen. Genet. 240:113 (1993);Content et al., “Expression and preliminary deletion analysis of the 42kDa 2-5A synthetase induced by human interferon,” in BiologicalInterferon Systems, Proceedings of ISIR-TNO Meeting on InterferonSystems, Cantell (ed.), pages 65-72 (Nijhoff 1987); Herschman, “The EGFReceptor,” in Control of Animal Cell Proliferation 1, Boynton et al.,(eds.) pages 169-199 (Academic Press 1985); Coumailleau et al., J. Biol.Chem. 270:29270 (1995); Fukunaga et al., J. Biol. Chem. 270:25291(1995); Yamaguchi et al., Biochem. Pharmacol. 50:1295 (1995); and Meiselet al., Plant Molec. Biol. 30:1 (1996).

Multiple amino acid substitutions can be made and tested using knownmethods of mutagenesis and screening, such as those disclosed byReidhaar-Olson and Sauer (Science 241:53-57, 1988) or Bowie and Sauer(Proc. Natl. Acad. Sci. USA 86:2152-2156, 1989). Briefly, these authorsdisclose methods for simultaneously randomizing two or more positions ina polypeptide, selecting for functional polypeptide, and then sequencingthe mutagenized polypeptides to determine the spectrum of allowablesubstitutions at each position. Other methods that can be used includephage display (e.g., Lowman et al., Biochem. 30:10832-10837, 1991;Ladner et al., U.S. Pat. No. 5,223,409; Huse, WIPO Publication WO92/06204) and region-directed mutagenesis (Derbyshire et al., Gene46:145, 1986; Ner et al., DNA 7:127, 1988).

Variants of the disclosed zsig63 DNA and polypeptide sequences can begenerated through DNA shuffling as disclosed by Stemmer, Nature370:389-91, 1994, Stemmer, Proc. Natl. Acad. Sci. USA 91:10747-51, 1994and WIPO Publication WO 97/20078. Briefly, variant DNAs are generated byin vitro homologous recombination by random fragmentation of a parentDNA followed by reassembly using PCR, resulting in randomly introducedpoint mutations. This technique can be modified by using a family ofparent DNAs, such as allelic variants or DNAs from different species, tointroduce additional variability into the process. Selection orscreening for the desired activity, followed by additional iterations ofmutagenesis and assay provides for rapid “evolution” of sequences byselecting for desirable mutations while simultaneously selecting againstdetrimental changes.

Mutagenesis methods as disclosed above can be combined withhigh-throughput, automated screening methods to detect activity ofcloned, mutagenized polypeptides in host cells. Mutagenized DNAmolecules that encode active polypeptides (e.g., anti-microbialactivity) can be recovered from the host cells and rapidly sequencedusing modem equipment. These methods allow the rapid determination ofthe importance of individual amino acid residues in a polypeptide ofinterest, and can be applied to polypeptides of unknown structure.

In addition, the proteins of the present invention (or polypeptidefragments thereof) can be joined to other bioactive molecules,particularly other cytokines, to provide multi-functional molecules. Forexample, one or more helices from zsig63 can be joined to othercytokines to enhance their biological properties or efficiency ofproduction.

The present invention thus provides a series of novel, hybrid moleculesin which a segment comprising one or more of the domains, coil-likestructure, or repeats, of zsig63 is fused to another polypeptide. Fusionis preferably done by splicing at the DNA level to allow expression ofchimeric molecules in recombinant production systems. The resultantmolecules are then assayed for such properties as improved solubility,improved stability, prolonged clearance half-life, improved expressionand secretion levels, and pharmacodynamics. Such hybrid molecules mayfurther comprise additional amino acid residues (e.g. a polypeptidelinker) between the component proteins or polypeptides.

Using the methods discussed above, one of ordinary skill in the art canidentify and/or prepare a variety of polypeptides that are substantiallysimilar to residues 16 to 219 of SEQ ID NO:2 or allelic variants thereofand retain the anti-microbial properties of the wild-type protein. Suchpolypeptides may include additional amino acids from affinity tags andthe like. Such polypeptides may also include additional polypeptidesegments as generally disclosed above.

The polypeptides of the present invention, including full-lengthproteins, fragments thereof and fusion proteins, can be produced ingenetically engineered host cells according to conventional techniques.However, host cells must be selected with some care as a result of theanti-microbial activity of the molecules of the present invention. Forexample, any cell culture-based system must be evaluated, because zsig63polypeptides, fragments, fusion proteins, antibodies, agonists orantagonists may kill the host cell as a part of an anti-microbialfunction. Zsig63 polypeptides are of a small enough size to permitpreparation by PCR or other protein chemistry techniques to avoid anypotential host cell toxicity problems. Alternatively, native orengineered precursor proteins, prior to post-translational cleavage toyield the mature zsig63 polypeptide, are inactive, thereby limiting hostcell cytotoxicity prior to lysosomal packaging. See, for example, Lehreret al., Cell 64: 229-30, 1991. Thus, precursor proteins to zsig63polypeptides may be produced in microbial cell culture.

Suitable host cells are those cell types that can be transformed ortransfected with exogenous DNA and grown in culture, and includebacteria, fungal cells, and cultured higher eukaryotic cells. Eukaryoticcells, particularly cultured cells of multicellular organisms, arepreferred. Techniques for manipulating cloned DNA molecules andintroducing exogenous DNA into a variety of host cells are disclosed bySambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, andAusubel et al. (eds.), Current Protocols in Molecular Biology, JohnWiley and Sons, Inc., New York, 1987.

In general, a DNA sequence encoding a zsig63 polypeptide of the presentinvention is operably linked to other genetic elements required for itsexpression, generally including a transcription promoter and terminatorwithin an expression vector. The vector will also commonly contain oneor more selectable markers and one or more origins of replication,although those skilled in the art will recognize that within certainsystems selectable markers may be provided on separate vectors, andreplication of the exogenous DNA may be provided by integration into thehost cell genome. Selection of promoters, terminators, selectablemarkers, vectors and other elements is a matter of routine design withinthe level of ordinary skill in the art. Many such elements are describedin the literature and are available through commercial suppliers.

To direct a zsig63 polypeptide into the secretory pathway of a hostcell, a secretory signal sequence (also known as a leader sequence,prepro sequence or pre sequence) is provided in the expression vector.The secretory signal sequence may be that of the zsig63 polypeptide,disclosed herein, or may be derived from another secreted protein (e.g.,t-PA) or synthesized de novo. The secretory signal sequence is joined tothe zsig63 polypeptide-encoding DNA sequence in the correct readingframe. Secretory signal sequences are commonly positioned 5′ to the DNAsequence encoding the polypeptide of interest, although certain signalsequences may be positioned elsewhere in the DNA sequence of interest(see, e.g., Welch et al., U.S. Pat. No. 5,037,743; Holland et al., U.S.Pat. No. 5,143,830).

Alternatively, the secretory signal sequence contained in thepolypeptides of the present invention is used to direct otherpolypeptides into the secretory pathway. The present invention providesfor such fusion polypeptides. A signal fusion polypeptide can be madewherein a secretory signal sequence derived from amino acid residues 1(Met) through 15 (Ala) of SEQ ID NO:2, is operably linked to anotherpolypeptide using methods known in the art and disclosed herein. Thesecretory signal sequence contained in the fusion polypeptides of thepresent invention is preferably fused amino-terminally to an additionalpeptide to direct the additional peptide into the secretory pathway.Such constructs have numerous applications known in the art. Forexample, these novel secretory signal sequence fusion constructs candirect the secretion of an active component of a normally non-secretedprotein. Such fusions may be used in vivo or in vitro to direct peptidesthrough the secretory pathway.

Cultured mammalian cells are also preferred hosts within the presentinvention. Methods for introducing exogenous DNA into mammalian hostcells include calcium phosphate-mediated transfection (Wigler et al.,Cell 14:725, 1978; Corsaro and Pearson, Somatic Cell Genetics 7:603,1981: Graham and Van der Eb, Virology 52:456, 1973), electroporation(Neumann et al., EMBO J. 1:841-845, 1982), DEAE-dextran mediatedtransfection (Ausubel et al., eds., Current Protocols in MolecularBiology, John Wiley and Sons, Inc., New York, 1987), liposome-mediatedtransfection (Hawley-Nelson et al., Focus 15:73, 1993; Ciccarone et al.,Focus 15:80, 1993), and viral vectors (A. Miller and G. Rosman,BioTechniques 7:980-90, 1989; Q. Wang and M. Finer, Nature Med.2:714-16, 1996). The production of recombinant polypeptides in culturedmammalian cells is disclosed, for example, by Levinson et al., U.S. Pat.No. 4,713,339; Hagen et al., U.S. Pat. No. 4,784,950; Palmiter et al.,U.S. Pat. No. 4,579,821; and Ringold, U.S. Pat. No. 4,656,134. Preferredcultured mammalian cells include the COS-1 (ATCC No. CRL 1650), COS-7(ATCC No. CRL 1651), BHK 570 (ATCC No. CRL 10314), 293 (ATCC No. CRL1573; Graham et al., J. Gen. Virol. 36:59-72, 1977) and Chinese hamsterovary (e.g. CHO-K1; ATCC No. CCL 61) cell lines. Additional suitablecell lines are known in the art and available from public depositoriessuch as the American Type Culture Collection, Rockville, Md. In general,strong transcription promoters are preferred, such as promoters fromSV-40 or cytomegalovirus. See, e.g., U.S. Pat. No. 4,956,288. Othersuitable promoters include those from metallothionein genes (U.S. Pat.Nos. 4,579,821 and 4,601,978) and the adenovirus major late promoter.

Drug selection is generally used to select for cultured mammalian cellsinto which foreign DNA has been inserted. Such cells are commonlyreferred to as “transfectants”. Cells that have been cultured in thepresence of the selective agent and are able to pass the gene ofinterest to their progeny are referred to as “stable transfectants.” Apreferred selectable marker is a gene encoding resistance to theantibiotic neomycin. Selection is carried out in the presence of aneomycin-type drug, such as G-418 or the like. Selection systems mayalso be used to increase the expression level of the gene of interest, aprocess referred to as “amplification.” Amplification is carried out byculturing transfectants in the presence of a low level of the selectiveagent and then increasing the amount of selective agent to select forcells that produce high levels of the products of the introduced genes.A preferred amplifiable selectable marker is dihydrofolate reductase,which confers resistance to methotrexate. Other drug resistance genes(e.g., hygromycin resistance, multi-drug resistance, puromycinacetyltransferase) can also be used. Alternative markers that introducean altered phenotype, such as green fluorescent protein, or cell surfaceproteins such as CD4, CD8, Class I MHC, placental alkaline phosphatasemay be used to sort transfected cells from untransfected cells by suchmeans as FACS sorting or magnetic bead separation technology.

Other higher eukaryotic cells can also be used as hosts, including plantcells, insect cells and avian cells. The use of Agrobacterium rhizogenesas a vector for expressing genes in plant cells has been reviewed bySinkar et al., J. Biosci. (Bangalore) 11:47-58, 1987. Transformation ofinsect cells and production of foreign polypeptides therein is disclosedby Guarino et al., U.S. Pat. No. 5,162,222 and WIPO publication WO94/06463. Insect cells can be infected with recombinant baculovirus,commonly derived from Autographa californica nuclear polyhedrosis virus(AcNPV). DNA encoding the zsig63 polypeptide is inserted into thebaculoviral genome in place of the ACNPV polyhedrin gene coding sequenceby one of two methods. The first is the traditional method of homologousDNA recombination between wild-type AcNPV and a transfer vectorcontaining the zsig63 flanked by AcNPV sequences. Suitable insect cells,e.g. SF9 cells, are infected with wild-type AcNPV and transfected with atransfer vector comprising a zsig63 polynucleotide operably linked to anAcNPV polyhedrin gene promoter, terminator, and flanking sequences. See,King and Possee, The Baculovirus Expression System: A Laboratory Guide,London, Chapman & Hall; O'Reilly et al., Baculovirus Expression Vectors:A Laboratory Manual, New York, Oxford University Press., 1994; and,Richardson, C. D., Ed., Baculovirus Expression Protocols. Methods inMolecular Biology, Totowa, N.J., Humana Press, 1995. Naturalrecombination within an insect cell will result in a recombinantbaculovirus which contains zsig63 driven by the polyhedrin promoter.Recombinant viral stocks are made by methods commonly used in the art.

The second method of making recombinant baculovirus utilizes atransposon-based system described by Luckow (Luckow et al., J. Virol.67:4566-79, 1993). This system is sold in the Bac-to-Bac kit (LifeTechnologies, Rockville, Md.). This system utilizes a transfer vector,pFastBacI™ (Life Technologies) containing a Tn7 transposon to move theDNA encoding the zsig63 polypeptide into a baculovirus genome maintainedin E. coli as a large plasmid called a “bacmid.” The pFastBacI™ transfervector utilizes the AcNPV polyhedrin promoter to drive the expression ofthe gene of interest, in this case zsig63. However, pFastBacI™ can bemodified to a considerable degree. The polyhedrin promoter can beremoved and substituted with the baculovirus basic protein promoter(also known as Pcor, p6.9 or MP promoter) which is expressed earlier inthe baculovirus infection, and has been shown to be advantageous forexpressing secreted proteins. See, Hill-Perkin and Possee, J. Gen.Virol. 71:971-6, 1990; Bonning. et al., J. Gen. Virol. 75:1551-6, 1994;and, Chazenbalk and Rapoport, J. Biol. Cherri. 270:1543-9, 1995. In suchtransfer vector constructs, a short or long version of the basic proteinpromoter can be used. Moreover, transfer vectors can be constructedwhich replace the native zsig63 secretory signal sequences withsecretory signal sequences derived from insect proteins. For example, asecretory signal sequence from Ecdysteroid Glucosyltransferase (EGT),honey bee Melittin (Invitrogen, Carlsbad, Calif.), or baculovirus gp67(PharMingen, San Diego, Calif.) can be used in constructs to replace thenative zsig63 secretory signal sequence. In addition, transfer vectorscan include an in-frame fusion with DNA encoding an epitope tag at theC- or N-terminus of the expressed zsig63 polypeptide, for example, aGlu-Glu epitope tag (Grussenmeyer et al., Proc. Natl. Acad. Sci.82:7952-4, 1985). Using a technique known in the art, a transfer vectorcontaining zsig63 is transformed into E. coli, and screened for bacmidswhich contain an interrupted lacZ gene indicative of recombinantbaculovirus. The bacmid DNA containing the recombinant baculovirusgenome is isolated, using common techniques, and used to transfectSpodoptera frugiperda cells, e.g. Sf9 cells. Recombinant virus thatexpresses zsig63 is subsequently produced. Recombinant viral stocks aremade by methods commonly used the art.

The recombinant virus is used to infect host cells, typically a cellline derived from the fall armyworm, Spodoptera frugiperda. See, ingeneral, Glick and Pasternak, Molecular Biotechnology: Principles andApplications of Recombinant DNA, ASM Press, Washington, D.C., 1994.Another suitable cell line is the High FiveO™ cell line (Invitrogen)derived from Trichoplusia ni (U.S. Pat. No. 5,300,435). Commerciallyavailable serum-free media are used to grow and maintain the cells.Suitable media are Sf900 II™ (Life Technologies) or ESF 921™ (ExpressionSystems) for the Sf9 cells; and Ex-cellO405™ (JRH Biosciences, Lenexa,Kans.) or Express FiveO™ (Life Technologies) for the T. ni cells. Thecells are grown up from an inoculation density of approximately 2-5×10⁵cells to a density of 1-2×10⁶ cells at which time a recombinant viralstock is added at a multiplicity of infection (MOI) of 0.1 to 10, moretypically near 3. The recombinant virus-infected cells typically producethe recombinant zsig63 polypeptide at 12-72 hours post-infection andsecrete it with varying efficiency into the medium. The culture isusually harvested 48 hours post-infection. Centrifugation is used toseparate the cells from the medium (supernatant). The supernatantcontaining the zsig63 polypeptide is filtered through micropore filters,usually 0.45 μm pore size. Procedures used are generally described inavailable laboratory manuals (King and Possee, ibid.; O'Reilly et al.,ibid.; Richardson, ibid.). Subsequent purification of the zsig63polypeptide from the supernatant can be achieved using methods describedherein.

Fungal cells, including yeast cells, can also be used within the presentinvention. Yeast species of particular interest in this regard includeSaccharomyces cerevisiae, Pichia pastoris, and Pichia methanolica.Methods for transforming S. cerevisiae cells with exogenous DNA andproducing recombinant polypeptides therefrom are disclosed by, forexample, Kawasaki, U.S. Pat. No. 4,599,311; Kawasaki et al., U.S. Pat.No. 4,931,373; Brake, U.S. Pat. No. 4,870,008; Welch et al., U.S. Pat.No. 5,037,743; and Murray et al., U.S. Pat. No. 4,845,075. Transformedcells are selected by phenotype determined by the selectable marker,commonly drug resistance or the ability to grow in the absence of aparticular nutrient (e.g., leucine). A preferred vector system for usein Saccharomyces cerevisiae is the POT1 vector system disclosed byKawasaki et al. (U.S. Pat. No. 4,931,373), which allows transformedcells to be selected by growth in glucose-containing media. Suitablepromoters and terminators for use in yeast include those from glycolyticenzyme genes (see, e.g., Kawasaki, U.S. Pat. No. 4,599,311; Kingsman etal., U.S. Pat. No. 4,615,974; and Bitter, U.S. Pat. No. 4,977,092) andalcohol dehydrogenase genes. See also U.S. Pat. Nos. 4,990,446;5,063,154; 5,139,936 and 4,661,454. Transformation systems for otheryeasts, including Hansenula polymorpha, Schizosaccharomyces pombe,Kluyveromyces lactis, Kluyveromyces fragilis, Ustilago maydis, Pichiapastoris, Pichia methanolica, Pichia guillermondii and Candida maltosaare known in the art. See, for example, Gleeson et al., J. Gen.Microbiol. 132:3459-65, 1986 and Cregg, U.S. Pat. No. 4,882,279.Aspergillus cells may be utilized according to the methods of McKnightet al., U.S. Pat. No. 4,935,349. Methods for transforming Acremoniumchrysogenum are disclosed by Sumino et al., U.S. Pat. No. 5,162,228.Methods for transforming Neurospora are disclosed by Lambowitz, U.S.Pat. No. 4,486,533.

The use of Pichia methanolica as host for the production of recombinantproteins is disclosed in WIPO Publications WO 97/17450, WO 97/17451, WO98/02536, and WO 98/02565. DNA molecules for use in transforming P.methanolica will commonly be prepared as double-stranded, circularplasmids, which are preferably linearized prior to transformation. Forpolypeptide production in P. methanolica, it is preferred that thepromoter and terminator in the plasmid be that of a P. methanolica gene,such as a P. methanolica alcohol utilization gene (AUG1 or AUG2). Otheruseful promoters include those of the dihydroxyacetone synthase (DHAS),formate dehydrogenase (FMD), and catalase (CAT) genes. To facilitateintegration of the DNA into the host chromosome, it is preferred to havethe entire expression segment of the plasmid flanked at both ends byhost DNA sequences. A preferred selectable marker for use in Pichiamethanolica is a P. methanolica ADE2 gene, which encodesphosphoribosyl-5-aminoimidazole carboxylase (AIRC; EC 4.1.1.21), whichallows ade2 host cells to grow in the absence of adenine. Forlarge-scale, industrial processes where it is desirable to minimize theuse of methanol, it is preferred to use host cells in which bothmethanol utilization genes (AUG1 and AUG2) are deleted. For productionof secreted proteins, host cells deficient in vacuolar protease genes(PEP4 and PRB1) are preferred. Electroporation is used to facilitate theintroduction of a plasmid containing DNA encoding a polypeptide ofinterest into P. methanolica cells. It is preferred to transform P.methanolica cells by electroporation using an exponentially decaying,pulsed electric field having a field strength of from 2.5 to 4.5 kV/cm,preferably about 3.75 kV/cm, and a time constant (t) of from 1 to 40milliseconds, most preferably about 20 milliseconds.

Prokaryotic host cells, including strains of the bacteria Escherichiacoli, Bacillus and other genera are also useful host cells within thepresent invention. Techniques for transforming these hosts andexpressing foreign DNA sequences cloned therein are well known in theart (see, e.g., Sambrook et al., ibid.). When expressing a zsig63polypeptide in bacteria such as E. coli, the polypeptide may be retainedin the cytoplasm, typically as insoluble granules, or may be directed tothe periplasmic space by a bacterial secretion sequence. In the formercase, the cells are lysed, and the granules are recovered and denaturedusing, for example, guanidine isothiocyanate or urea. The denaturedpolypeptide can then be refolded and dimerized by diluting thedenaturant, such as by dialysis against a solution of urea and acombination of reduced and oxidized glutathione, followed by dialysisagainst a buffered saline solution. In the latter case, the polypeptidecan be recovered from the periplasmic space in a soluble and functionalform by disrupting the cells (by, for example, sonication or osmoticshock) to release the contents of the periplasmic space and recoveringthe protein, thereby obviating the need for denaturation and refolding.

Transformed or transfected host cells are cultured according toconventional procedures in a culture medium containing nutrients andother components required for the growth of the chosen host cells. Avariety of suitable media, including defined media and complex media,are known in the art and generally include a carbon source, a nitrogensource, essential amino acids, vitamins and minerals. Media may alsocontain such components as growth factors or serum, as required. Thegrowth medium will generally select for cells containing the exogenouslyadded DNA by, for example, drug selection or deficiency in an essentialnutrient which is complemented by the selectable marker carried on theexpression vector or co-transfected into the host cell. P. methanolicacells are cultured in a medium comprising adequate sources of carbon,nitrogen and trace nutrients at a temperature of about 25° C. to 35° C.Liquid cultures are provided with sufficient aeration by conventionalmeans, such as shaking of small flasks or sparging of fermentors. Apreferred culture medium for P. methanolica is YEPD (2% D-glucose, 2%Bacto™ Peptone (Difco Laboratories, Detroit, Mich.), 1% Bacto™ yeastextract (Difco Laboratories), 0.004% adenine and 0.006% L-leucine).

Expressed recombinant zsig63 polypeptides (or chimeric zsig63polypeptides) can be purified using fractionation and/or conventionalpurification methods and media. Ammonium sulfate precipitation and acidor chaotrope extraction may be used for fractionation of samples.Exemplary purification steps may include hydroxyapatite, size exclusion,FPLC and reverse-phase high performance liquid chromatography. Suitableanion exchange media include derivatized dextrans, agarose, cellulose,polyacrylamide, specialty silicas, and the like. PEI, DEAE, QAE and Qderivatives are preferred, with DEAE Fast-Flow Sepharose (Pharmacia,Piscataway, N.J.) being particularly preferred. Exemplarychromatographic media include those media derivatized with phenyl,butyl, or octyl groups, such as Phenyl-Sepharose FF (Pharmacia),Toyopearl butyl 650 (Toso Haas, Montgomeryville, Pa.), Octyl-Sepharose(Pharmacia) and the like; or polyacrylic resins, such as Amberchrom CG71 (Toso Haas) and the like. Suitable solid supports include glassbeads, silica-based resins, cellulosic resins, agarose beads,cross-linked agarose beads, polystyrene beads, cross-linkedpolyacrylamide resins and the like that are insoluble under theconditions in which they are to be used. These supports may be modifiedwith reactive groups that allow attachment of proteins by amino groups,carboxyl groups, sulfhydryl groups, hydroxyl groups and/or carbohydratemoieties. Examples of coupling chemistries include cyanogen bromideactivation, N-hydroxysuccinimide activation, epoxide activation,sulfhydryl activation, hydrazide activation, and carboxyl and aminoderivatives for carbodiimide coupling chemistries. These and other solidmedia are well known and widely used in the art, and are available fromcommercial suppliers. Methods for binding receptor polypeptides tosupport media are well known in the art. Selection of a particularmethod is a matter of routine design and is determined in part by theproperties of the chosen support. See, for example, AffinityChromatography: Principles & Methods, Pharmacia LKB Biotechnology,Uppsala, Sweden, 1988.

The polypeptides of the present invention can be isolated byexploitation of their structural and biological properties. For example,immobilized metal ion adsorption (IMAC) chromatography can be used topurify histidine-rich proteins or proteins having a His-affinity tag.Briefly, a gel is first charged with divalent metal ions to form achelate (Sulkowski, Trends in Biochem. 3:1-7, 1985). Histidine-richproteins will be adsorbed to this matrix with differing affinities,depending upon the metal ion used, and will be eluted by competitiveelution, lowering the pH, or use of strong chelating agents. Othermethods of purification include purification of glycosylated proteins bylectin affinity chromatography and ion exchange chromatography (Methodsin Enzymol., Vol. 182, “Guide to Protein Purification”, M. Deutscher,(ed.), Acad. Press, San Diego, 1990, pp.529-39). Within additionalembodiments of the invention, a fusion of the polypeptide of interestand an affinity tag (e.g., maltose-binding protein, an immunoglobulindomain) may be constructed to facilitate purification.

Protein refolding (and optionally reoxidation) procedures may beadvantageously used. It is preferred to purify the protein to >80%purity, more preferably to >90% purity, even more preferably >95%, andparticularly preferred is a pharmaceutically pure state, that is greaterthan 99.9% pure with respect to contaminating macromolecules,particularly other proteins and nucleic acids, and free of infectiousand pyrogenic agents. Preferably, a purified protein is substantiallyfree of other proteins, particularly other proteins of animal origin.

zsig63 polypeptides or fragments thereof may also be prepared throughchemical synthesis. zsig63 polypeptides may be monomers or multimers;glycosylated or non-glycosylated; pegylated or non-pegylated; amidatedor non-amidated; sulfated or non-sulfated; and may or may not include aninitial methionine amino acid residue.

Polypeptides of the present invention can also be synthesized byexclusive solid phase synthesis, partial solid phase methods, fragmentcondensation or classical solution synthesis. Methods for synthesizingpolypeptides are well known in the art. See, for example, Merrifield, J.Am. Chem. Soc. 85:2149, 1963;

Kaiser et al., Anal. Biochem. 34:595, 1970. After the entire synthesisof the desired peptide on a solid support, the peptide-resin is washedwith a reagent which cleaves the polypeptide from the resin and removesmost of the side-chain protecting groups. Such methods are wellestablished in the art.

Molecules of the present invention can be used to identify and isolatereceptors that bind zsig63 polypeptide. For example, proteins andpeptides of the present invention can be immobilized on a column andmembrane preparations run over the column (Immobilized Affinity LigandTechniques, Hermanson et al., eds., Academic Press, San Diego, Calif.,1992, pp.195-202). Proteins and peptides can also be radiolabeled(Methods in Enzymol., vol. 182, “Guide to Protein Purification”, M.Deutscher, ed., Acad. Press, San Diego, 1990, 721-37) or photoaffinitylabeled (Brunner et al., Ann. Rev. Biochem. 62:483-514, 1993 and Fedanet al., Biochem. Pharmacol. 33:1167-80, 1984) and specific cell-surfaceproteins can be identified.

An assay system that uses a ligand-binding receptor (or an antibody, onemember of a complement/anti-complement pair) or a binding fragmentthereof, and a commercially available biosensor instrument (BIAcore™,Pharmacia Biosensor, Piscataway, N.J.) may be advantageously employed.Such receptor, antibody, member of a complement/anti-complement pair orfragment is immobilized onto the surface of a receptor chip. Use of thisinstrument is disclosed by Karlsson, J. Immunol. Methods 145:229-40,1991 and Cunningham and Wells, J. Mol. Biol. 234:554-63, 1993. Areceptor, antibody, member or fragment is covalently attached, usingamine or sulfhydryl chemistry, to dextran fibers that are attached togold film within the flow cell. A test sample is passed through thecell. If a ligand, epitope, or opposite member of thecomplement/anti-complement pair is present in the sample, it will bindto the immobilized receptor, antibody or member, respectively, causing achange in the refractive index of the medium, which is detected as achange in surface plasmon resonance of the gold film. This system allowsthe determination of on- and off-rates, from which binding affinity canbe calculated, and assessment of stoichiometry of binding.

Ligand-binding receptor polypeptides can also be used within other assaysystems known in the art. Such systems include Scatchard analysis fordetermination of binding affinity (see Scatchard, Ann. NY Acad. Sci. 51:660-72, 1949) and calorimetric assays (Cunningham et al., Science253:545-48, 1991; Cunningham et al., Science 245:821-25, 1991).

In another embodiment, polypeptide-toxin fusion proteins orantibody-toxin fusion proteins can be used for targeted cell or tissueinhibition or ablation (for instance, to treat cancer cells or tissues).Alternatively, if the polypeptide has multiple functional domains (i.e.,an activation domain or a receptor binding domain, plus a targetingdomain), a fusion protein including only the targeting domain may besuitable for directing a detectable molecule, a cytotoxic molecule or acomplementary molecule to a cell or tissue type of interest. Ininstances where the domain only fusion protein includes a complementarymolecule, the anti-complementary molecule can be conjugated to adetectable or cytotoxic molecule. Such domain-complementary moleculefusion proteins thus represent a generic targeting vehicle forcell/tissue-specific delivery of genericanti-complementary-detectable/cytotoxic molecule conjugates.

In another embodiment, zsig63-cytokine fusion proteins orantibody-cytokine fusion proteins can be used for enhancing in vivokilling of target tissues (for example, blood and bone marrow cancers),if the zsig63 polypeptide or anti-zsig63 antibody targets thehyperproliferative blood or bone marrow cell (See, generally, Hornick etal., Blood 89:4437-47, 1997). Hornick et al. described fusion proteinsthat target a cytokine to a desired site of action, thereby providing anelevated local concentration of cytokine. Suitable zsig63 polypeptidesor anti-zsig63 antibodies can target an undesirable cell or tissue(i.e., a tumor or a leukemia), and the fused cytokine can mediateimproved target cell lysis by effector cells. Suitable cytokines forthis purpose include interleukin 2 and granulocyte-macrophagecolony-stimulating factor (GM-CSF), for instance.

In yet another embodiment, if the zsig63 polypeptide or anti-zsig63antibody targets vascular cells or tissues, such polypeptide or antibodymay be conjugated with a radionuclide, and particularly with abeta-emitting radionuclide, to reduce restenosis. Such therapeuticapproach poses less danger to clinicians who administer the radioactivetherapy. For instance, iridium-192 impregnated ribbons placed intostented vessels of patients until the required radiation dose wasdelivered showed decreased tissue growth in the vessel and greaterluminal diameter than the control group, which received placebo ribbons.Further, revascularisation and stent thrombosis were significantly lowerin the treatment group. Similar results are predicted with targeting ofa bioactive conjugate containing a radionuclide, as described herein.

The bioactive polypeptide or antibody conjugates described herein can bedelivered intravenously, intraarterially or intraductally, or may beintroduced locally at the intended site of action.

Another aspect of the present invention includes zsig63 polypeptidefragments. Preferred fragments include the leader sequence, ranging fromamino acid 1 (Met) to amino acid 15 (Ala) of SEQ ID NO:2. Such leadersequences may be used to direct the secretion of other polypeptides.Such fragments of the present invention may be used as follows: thealternative secretion leader fragments are formed as fusion proteinswith alternative proteins selected for secretion; plasmids bearingregulatory regions capable of directing the expression of the fusionprotein are introduced into test cells; and secretion of the protein ismonitored.

Moreover, using methods described in the art, polypeptide fusions, orhybrid zsig63 proteins, are constructed using regions or domains ofzsig63 in combination with those of paralogs, orthologs, or heterologousproteins (Sambrook et al., ibid., Altschul et al., ibid., Picard. D.,Cur. Opin. Biology, 5:511-515, 1994, and references therein). Thesemethods allow the determination of the biological importance of largerdomains or regions in a polypeptide of interest. Such hybrids may alterreaction kinetics, binding, constrict or expand the substratespecificity, or alter tissue and cellular localization of a polypeptide,and can be applied to polypeptides of unknown structure.

Fusion polypeptides can be prepared by methods known to those skilled inthe art by preparing each component of the fusion protein and chemicallyconjugating them. Alternatively, a polynucleotide encoding one or morecomponents of the fusion protein in the proper reading frame can begenerated using known techniques and expressed by the methods describedherein. For example, part or all of a domain(s) conferring a biologicalfunction may be swapped between zsig63 of the present invention with thefunctionally equivalent domain(s) from another family member. Suchdomains include, but are not limited to the secretory signal sequence,and domains 1 through 3, and the coil-like structure, described herein.Such fusion proteins would be expected to have a biological functionalprofile that is the same or similar to polypeptides of the presentinvention or other known family proteins or to a heterologous protein,depending on the fusion constructed. Moreover, such fusion proteins mayexhibit other properties as disclosed herein.

Standard molecular biological and cloning techniques can be used to swapthe equivalent domains between the zsig63 polypeptide and thosepolypeptides to which they are fused. Generally, a DNA segment thatencodes a domain of interest, e.g., a zsig63 domain 1, 2, or 3, or amotif described herein, is operably linked in frame to at least oneother DNA segment encoding an additional polypeptide and inserted intoan appropriate expression vector, as described herein. Generally DNAconstructs are made such that the several DNA segments that encode thecorresponding regions of a polypeptide are operably linked in frame tomake a single construct that encodes the entire fusion protein, or afunctional portion thereof. For example, a DNA construct would encodefrom N-terminus to C-terminus a fusion protein comprising a signalpolypeptide followed by a mature polypeptide; or a DNA construct wouldencode from N-terminus to C-terminus a fusion protein comprising asignal polypeptide followed by domain-1, followed by domain-2, followedby domain-3, or as interchanged with equivalent regions from anotherprotein. Such fusion proteins can be expressed, isolated, and assayedfor activity as described herein. Polypeptide linkers are preferablyemployed if necessary to provide separation of component polypeptides ofthe fusion or to allow for flexibility of the fusion protein, therebypreserving the anti-microbial activity of each defensin component of thefusion protein. Those of ordinary skill in the art are capable ofdesigning such linkers.

Within another aspect of the present invention there is provided apharmaceutical composition comprising purified zsig63 polypeptide incombination with a pharmaceutically acceptable vehicle. Suchpharmaceutical compositions are used in the treatment of conditionsassociated with pathological microbes, including bacterial, fungal andviral infections. Antibacterial applications of zsig63 polypeptideinclude situations where the pathogen has become resistant to standardtreatments. For example, hospital sepsis is an increasing problem, sinceStaphylococcus and other bacterial and microbial strains have becomeresistant to commonly used antibiotics.

In general, anti-microbial activity of zsig63 polypeptides, fragments,fusions, antibodies, agonists and antagonists can be evaluated bytechniques that are known in the art. More specifically, anti-microbialactivity can be assayed by evaluating the sensitivity of microbial cellcultures to test agents and by evaluating the protective effect of testagents on infected mice. See, for example, Musiek et al., Antimicrob.Agents Chemothr. 3: 40, 1973. Antiviral activity can also be assessed byprotection of mammalian cell cultures. Known techniques for evaluatinganti-microbial activity include, for example, Barsum et al., Eur.Respir. J. 8(5): 709-14, 1995; Sandovsky-Losica et al., J. Med. Vet.Mycol (England) 28(4): 279-87, 1990; Mehentee et al., J. Gen. Microbiol(England) 135 (Pt. 8): 2181-8, 1989; Segal and Savage, Journal ofMedical and Veterinary Mycology 24: 477-479, 1986 and the like. Knownassays specific for anti-viral activity include, for example, thosedescribed by Daher et al., J. Virol. 60(3): 1068-74, 1986.

In addition, contract laboratories offer services in evaluatinganti-microbial properties. For example, Panlabs, Inc. of Bothell, Wash.offer in vitro or in vivo testing for bacteria, gram negative(Enterobacter cloacae, Escherichia coli, Klebsiella pneumonia, Proteusvulgaris, Pseudomonas aeruginosa, Salmonella typhimurium and Serratiamarcescēns), gram positive (Bacillus subtilis, Brevebacteriumammoniagenes, Corynebacterium minutissimum, Micrococcus luteus,Mycobacterium ranae, Staphylococcus strains and Streptococcus strains)and anaerobic organisms (Actinomyces viscosus, Bacteroides fragilis,Clostridium sporogenes, Corynebacterium acnes, Helicobacter pylori andPorphyromonas gingivalis), as well as for protozoa (Trichomonas foetus)and fungi (e.g., Candida albicans, Epidermophyton floccosum, Exophialajeanselmei, Microsporum strains, Trichophyton strains and the like).Also, Molecular Probes of Oregon has commercially available fluorescencetechnology for use in bacteriology.

If desired, zsig63 polypeptide, fragment, fusion protein, agonist,antagonist or antibody performance in this regard can be compared toproteins known to be functional in this regard, such as proline-richproteins, lysozyme, histatins, lactoperoxidase or the like. In addition,zsig63 polypeptide, fragment, fusion protein, antibody, agonist orantagonist may be evaluated in combination with one or moreanti-microbial agents to identify synergistic effects.

High expression of zsig63 in salivary gland suggests that anti-microbialpolypeptides of the present invention can be used for treatment ofdental carries (tooth decay), periodontal disease, thrush, andgastrointestinal disease. Other applications can be used in urinarytract infections, vaginal infections, prevention of infection in skinand other epithelial wounds. As such, the polypeptides of the presentinvention can help establish normal microflora and protect againstpathogenic colonization and invasion.

Moreover, microorganisms have specific infective stages where theydecorate their surface with proline coil containing proteins. One theoryis that they are decoying or evading the host immune system byexpressing host-like, but inactive, proteins on their surfaces. Thezsig63 polypeptide of the present invention can be one of these hostpolypeptides that the microorganism is mimicking. Moreover, there may bea correlation with Zinc and resistance to microbial infection. If zsig63binds zinc (or some other cation) there may be a delivery function, orimmune activation function with zinc as a co-factor for regulation ofspecific cell types, or defensive enzymes. Such immune activation byzsig63 polypeptides can be assessed by assays that are well known in theart.

The pharmaceutical compositions of the present invention may also beused when pro-inflammatory activity is desired. Applications for suchpro-inflammatory activity include the treatment of chronic tissuedamage, particularly in areas having a limited or damaged vascularsystem, e.g., damage in extremities associated with diabetes. Incontrast, antagonists to zsig63 polypeptides may be useful asanti-inflammatory agents.

Zsig63 polypeptide pharmaceutical compositions of the present inventionmay also be used in the treatment of conditions where stimulation ofimmune responsiveness is desired. Such conditions include the treatmentof patients having incompetent immune systems, such as AIDS patients orindividuals that have undergone chemotherapy, radiation treatment or thelike.

Because zsig63 polypeptide was found in a salivary gland library andcystic fibrosis is characterized by frequent microbial infection,pharmaceutical compositions containing zsig63 polypeptide are alsocontemplated for use in the treatment of lung infections associated withcystic fibrosis. Also contemplated by the present invention areengineered zsig63 polypeptides that are characterized by decreasedsensitivity to salt concentration. Decreased sensitivity to high saltconcentration will preserve anti-microbial activity of engineered zsig63polypeptides in high salt environments, such as in the lung airways ofpatients suffering from cystic fibrosis. In this manner, pharmaceuticalcompositions containing engineered zsig63 polypeptides that areformulated for delivery to the lungs can be used to treat lunginfections associated with cystic fibrosis.

Another aspect of the present invention involves the detection of zsig63polypeptides in cell culture or in a serum sample or tissue biopsy of apatient undergoing evaluation for SPG, Chediak-Higashi syndrome, orother conditions characterized by an alteration in defensinconcentration. Zsig63 polypeptides can be detected using immunoassaytechniques and antibodies capable of recognizing a zsig63 polypeptideepitope, as described herein. More specifically, the present inventioncontemplates methods for detecting zsig63 polypeptide comprising:

exposing a solution or sample or cell culture lysate or supernatant,possibly containing zsig63 polypeptide, to an antibody attached to asolid support, wherein said antibody binds to a first epitope of azsig63 polypeptide;

washing said immobilized antibody-polypeptide to remove unboundcontaminants;

exposing the immobilized antibody-polypeptide to a second antibodydirected to a second epitope of a zsig63 polypeptide, wherein the secondantibody is associated with a detectable label; and

detecting the detectable label. Zsig63 polypeptide concentrationdiffering from that of controls may be indicative of SPG,Chediak-Higashi syndrome or other conditions characterized by analteration in defensin concentration. In addition, expression of zsig63may be monitored in cystic fibrosis patients as a predictor of the onsetof infectious crises. Also, high defensin levels have been associatedwith cytotoxic effects in lung, indicating that other hostanti-microbial polypeptides, such as zsig63 polypeptide levels can beused as indicators for disease onset and cytotoxicity, and used todirect treatment for averting or addressing such cytotoxicity. Forexample, antibodies directed to zsig63 polypeptide can be administeredto inactivate the same in a treatment modality.

Within additional aspects of the invention there are provided antibodiesor synthesized binding proteins(e.g., those generated by phage display,E. coli Fab, and the like) that specifically bind to the zsig63polypeptides described above. Such antibodies are useful for, amongother uses as described herein, preparation of anti-idiotypicantibodies. Synthesized binding proteins may be produced by phagedisplay using commercially available kits, such as the Ph.D.™ PhageDisplay Peptide Library Kits available from New England Biolabs, Inc.(Beverly, Mass.). Phage display techniques are described, for example,in U.S. Pat. Nos. 5,223,409, 5,403,484 and 5,571,698.

An additional aspect of the present invention provides methods foridentifying agonists or antagonists of the zsig63 polypeptides disclosedabove, which agonists or antagonists may have valuable properties asdiscussed further herein. Within one embodiment, there is provided amethod of identifying zsig63 polypeptide agonists, comprising providingcells responsive thereto, culturing the cells in the presence of a testcompound and comparing the cellular response with the cell cultured inthe presence of the zsig63 polypeptide, and selecting the test compoundsfor which the cellular response is of the same type.

Within another embodiment, there is provided a method of identifyingantagonists of zsig63 polypeptide, comprising providing cells responsiveto a zsig63 polypeptide, culturing a first portion of the cells in thepresence of zsig63 polypeptide, culturing a second portion of the cellsin the presence of the zsig63 polypeptide and a test compound, anddetecting a decrease in a cellular response of the second portion of thecells as compared to the first portion of the cells.

A further aspect of the invention provides a method of studyingchemoattraction of monocytes in cell culture, comprising incubatingmonocytes in a culture medium comprising a zsig63 polypeptide, fragment,fusion protein, antibody, agonist or antagonist to study or evaluatemonocyte chemoattraction. Such evaluation may be conducted using methodsknown in the art, such as those described by Territo et al. referencedabove.

Melanocortin receptors are G-coupled protein receptors which activateadenylate cyclase and cause calcium flux. The agouti protein (whichcontains a 36 amino acid domain that is toxin-like) is thought toinhibit the binding of MSH-alpha to MC1 and MC4. In addition, the agoutiprotein is thought to be an antagonist of calcium channels, and certaintoxins are believed to modulate ion flux. Experimental evidence has beengenerated, suggesting that defensins are capable of blocking calciumchannels. Similarly, zsig63 polypeptides could have such properties.

A further aspect of the invention provides a method of studying activityof the melanocortin family of receptors in cell culture, comprisingincubating cells that endogenously bear such receptors (e.g., ACTHreceptors or the like) or cells that have been engineered to bear suchreceptors in a culture medium comprising a ligand or putative ligand andzsig63 polypeptide, fragment, fusion protein, antibody, agonist orantagonist to study or evaluate ligand or putative ligand binding and/orion flux regulation or modulation. Such evaluation may be conductedusing methods known in the art, such as those described by Zhu et al.referenced above.

A further aspect of the invention provides a method of studying ion fluxin cell culture, comprising incubating cells that are capable of ionflux, such as calcium flux, sodium flux, potassium flux or the like, ina culture medium comprising zsig63 polypeptide, fragment, fusionprotein, antibody, agonist or antagonist to study or evaluate ion fluxregulation or modulation.

A further aspect of the invention provides a method of studyingcytocidal activity against mammalian cells, such as tumor cells, in cellculture, comprising incubating such cells in a culture medium comprisinga zsig63 polypeptide, fragment, fusion protein, antibody, agonist orantagonist at high test agent and low cell concentration to study orevaluate cytocidal activity. Such evaluation may be conducted usingmethods known in the art, such as those described by Lichtenstein etal., Blood 68: 1407-10, 1986 and Sheu et al., Antimicrob. AgentsChemother. 28: 626-9, 1993.

Another aspect of the present invention involves the use of zsig63polypeptides, fragments, fusion proteins or agonists as cell culturereagents in in vitro studies of exogenous microorganism infection, suchas bacterial, viral or fungal infection. Such moieties may also be usedin in vivo animal models of infection.

An additional aspect of the present invention is to study epithelialcell defensin induction in cell culture. In this aspect of the presentinvention, epithelial cells are cultured and exposed to pathogenicstimuli. Induction of zsig63 polypeptide production by the epithelialcells is then measured.

A high level of expression of zsig63 polypeptide was observed byNorthern blot in the trachea and by dot blot in the salivary gland andtrachea. Consequently, another aspect of the present invention involvesthe detection of zsig63 polypeptides in the serum or tissue biopsy of apatient undergoing evaluation for salivary gland function ordysfunction. Such zsig63 polypeptides can be detected using immunoassaytechniques and antibodies capable of recognizing zsig63 polypeptideepitopes.

More specifically, the present invention contemplates methods fordetecting zsig63 polypeptide comprising:

exposing a solution possibly containing zsig63 polypeptide to anantibody attached to a solid support, wherein said antibody binds to afirst epitope of a zsig63 polypeptide;

washing said immobilized antibody-polypeptide to remove unboundcontaminants;

exposing the immobilized antibody-polypeptide to a second antibodydirected to a second epitope of a zsig63 polypeptide, wherein the secondantibody is associated with a detectable label; and

detecting the detectable label. Changes in serum or biopsy zsig63polypeptide concentration (relative to normal serum or tissueconcentration) may be indicative of dysfunction of the salivary gland.

Salivary gland dysfunction includes digestive dysfunction, wound healingdysfunction, inadequate saliva production or composition, mucosalintegrity breakdown, and failure of or diminished anti-microbialfunction. Detection of zsig63 polypeptide at relatively high levels inthe trachea may indicate that such polypeptides may serve as a marker oflung dysfunction. Moreover, zsig63 expression is detected in lung.Examples of conditions associated with salivary gland or lungdysfunction include salivary gland carcinoma, sarcoidosis, pneumocysticcarinii (particularly as associated with AIDS patients), emphysema,chronic bronchitis, cystic fibrosis, ARDS, SIDS or the like. Inaddition, zsig63 polypeptides are expressed in the prostate at a levelsimilar to trachea, as well as in the salivary gland. The prostate glandis androgen regulated and shares other properties with salivary glands.Consequently, dysfunction thereof, such as prostate adenocarcinoma orthe like, may also be detected using zsig63 polypeptides or zsig63antibodies.

Also, the salivary glands synthesize and secrete a number of proteinshaving diverse biological functions. Such proteins facilitatelubrication of the oral cavity (e.g., mucins and proline-rich proteins),remineralization (e.g., statherin and ionic proline-rich proteins) anddigestion (e.g., amylase, lipase and proteases) and provideanti-microbial (e.g., proline-rich proteins, lysozyme, histatins andlactoperoxidase) and mucosal integrity maintenance (e.g., mucins)capabilities. In addition, saliva is a rich source of growth factorssynthesized by the salivary glands. For example, saliva is known tocontain epidermal growth factor (EGF), nerve growth factor (NGF),transforming growth factor-alpha (TGF-α), transforming growthfactor-beta (TGF-β), insulin, insulin-like growth factors I and II(IGF-I and IGF-II) and fibroblast growth factor (FGF). See, for example,Zelles et al., J. Dental. Res. 74(12): 1826-32, 1995. Synthesis ofgrowth factors by the salivary gland is believed to beandrogen-dependent and to be necessary for the health of the oral cavityand gastrointestinal tract.

Thus, zsig63 polypeptides, agonists or antagonists thereof may betherapeutically useful for aiding digestion. To verify the presence ofthis capability in zsig63 polypeptides, agonists or antagonists of thepresent invention, such zsig63 polypeptides, agonists or antagonists areevaluated with respect to their ability to break down starch accordingto procedures known in the art. If desired, zsig63 polypeptideperformance in this regard can be compared to digestive enzymes, such asamylase, lipase, proteases and the like. In addition, zsig63polypeptides or agonists or antagonists thereof may be evaluated incombination with one or more digestive enzymes to identify synergisticeffects.

The activity of molecules of the present invention can be measured usinga variety of assays that measure stimulation of gastrointestinal cellcontractility, modulation of nutrient uptake and/or secretion ofdigestive enzymes. Of particular interest are changes in contractilityof smooth muscle cells. For example, the contractile response ofsegments of mammalian duodenum or other gastrointestinal smooth musclestissue (Depoortere et al., J. Gastrointestinal Motility 1:150-159,1989). An exemplary in vivo assay uses an ultrasonic micrometer tomeasure the dimensional changes radially between commissures andlongitudinally to the plane of the valve base (Hansen et al., Society ofThoracic Surgeons 60:S384-390, 1995).

An in vivo approach for assaying proteins of the present inventioninvolves viral delivery systems. Exemplary viruses for this purposeinclude adenovirus, herpesvirus, retroviruses, vaccinia virus, andadeno-associated virus (AAV). Adenovirus, a double-stranded DNA virus,is currently the best studied gene transfer vector for delivery ofheterologous nucleic acid (for review, see T. C. Becker et al., Meth.Cell Biol. 43:161-89, 1994; and J. T. Douglas and D. T. Curiel, Science& Medicine 4:44-53, 1997). The adenovirus system offers severaladvantages: (i) adenovirus can accommodate relatively large DNA inserts;(ii) can be grown to high-titer; (iii) infect a broad range of mammaliancell types; and (iv) can be used with many different promoters includingubiquitous, tissue specific, and regulatable promoters. Also, becauseadenoviruses are stable in the bloodstream, they can be administered byintravenous injection.

Using adenovirus vectors where portions of the adenovirus genome aredeleted, inserts are incorporated into the viral DNA by direct ligationor by homologous recombination with a co-transfected plasmid. In anexemplary system, the essential E1 gene has been deleted from the viralvector, and the virus will not replicate unless the E1 gene is providedby the host cell (the human 293 cell line is exemplary). Whenintravenously administered to intact animals, adenovirus primarilytargets the liver. If the adenoviral delivery system has an E1 genedeletion, the virus cannot replicate in the host cells. However, thehost's tissue (e.g., liver) will express and process (and, if asecretory signal sequence is present, secrete) the heterologous protein.Secreted proteins will enter the circulation in the highly vascularizedliver, and effects on the infected animal can be determined.

Moreover, adenoviral vectors containing various deletions of viral genescan be used in an attempt to reduce or eliminate immune responses to thevector. Such adenoviruses are E1 deleted, and in addition containdeletions of E2A or E4 (Lusky, M. et al., J. Virol. 72:2022-2032, 1998;Raper, S. E. et al., Human Gene Therapy 9:671-679, 1998). In addition,deletion of E2b is reported to reduce immune responses (Amalfitano, A.et al., J. Virol. 72:926-933, 1998). Moreover, by deleting the entireadenovirus genome, very large inserts of heterologous DNA can beaccommodated. Generation of so called “gutless” adenoviruses where allviral genes are deleted are particularly advantageous for insertion oflarge inserts of heterologous DNA. For review, see Yeh, P. andPerricaudet, M., FASEB J. 11:615-623, 1997.

The adenovirus system can also be used for protein production in vitro.By culturing adenovirus-infected non-293 cells under conditions wherethe cells are not rapidly dividing, the cells can produce proteins forextended periods of time. For instance, BHK cells are grown toconfluence in cell factories, then exposed to the adenoviral vectorencoding the secreted protein of interest. The cells are then grownunder serum-free conditions, which allows infected cells to survive forseveral weeks without significant cell division. Alternatively,adenovirus vector infected 293 cells can be grown as adherent cells orin suspension culture at relatively high cell density to producesignificant amounts of protein (See Garnier et al., Cytotechnol.15:145-55, 1994). With either protocol, an expressed, secretedheterologous protein can be repeatedly isolated from the cell culturesupernatant, lysate, or membrane fractions depending on the dispositionof the expressed protein in the cell. Within the infected 293 cellproduction protocol, non-secreted proteins may also be effectivelyobtained.

Compounds identified as zsig63 agonists are useful in vitro and in vivo.For example, zsig63 and agonist compounds are useful as components ofdefined cell culture media, and may be used alone or in combination withother cytokines and hormones to replace serum that is commonly used incell culture. Thus, zsig63 polypeptides and zsig63 agonist polypeptidesare useful as a research reagent, such as for the expansion of culturedcells. As such, zsig63 polypeptides are added to tissue culture mediafor these cell types.

As a ligand, the activity of zsig63 polypeptide can be measured by asilicon-based biosensor microphysiometer which measures theextracellular acidification rate or proton excretion associated withreceptor binding and subsequent physiologic cellular responses. Anexemplary device is the Cytosensor™ Microphysiometer manufactured byMolecular Devices, Sunnyvale, Calif. A variety of cellular responses,such as cell proliferation, ion transport, energy production,inflammatory response, regulatory and receptor activation, and the like,can be measured by this method. See, for example, McConnell, H. M. etal., Science 257:1906-1912, 1992; Pitchford, S. et al., Meth. Enzymol.228:84-108, 1997; Arimilli, S. et al., J. Immunol. Meth. 212:49-59,1998; Van Liefde, I. et al., Eur. J. Pharmacol. 346:87-95, 1998. Themicrophysiometer can be used for assaying adherent or non-adherenteukaryotic or prokaryotic cells. By measuring extracellularacidification changes in cell media over time, the microphysiometerdirectly measures cellular responses to various stimuli, includingzsig63 polypeptide, its agonists, or antagonists. Preferably, themicrophysiometer is used to measure responses of a zsig63-responsiveeukaryotic cell, compared to a control eukaryotic cell that does notrespond to zsig63 polypeptide. Zsig63-responsive eukaryotic cellscomprise cells into which a receptor for zsig63 has been transfectedcreating a cell that is responsive to zsig63; or cells naturallyresponsive to zsig63 such as cells derived from, for example, pancreas,intestinal, prostate or tracheal tissue. Differences, measured by achange, for example, an increase or diminution in extracellularacidification, in the response of cells exposed to zsig63 polypeptide,relative to a control not exposed to zsig63, are a direct measurement ofzsig63-modulated cellular responses. Moreover, such zsig63-modulatedresponses can be assayed under a variety of stimuli. Using themicrophysiometer, there is provided a method of identifying agonists ofzsig63 polypeptide, comprising providing cells responsive to a zsig63polypeptide, culturing a first portion of the cells in the absence of atest compound, culturing a second portion of the cells in the presenceof a test compound, and detecting a change, for example, an increase ordiminution, in a cellular response of the second portion of the cells ascompared to the first portion of the cells. The change in cellularresponse is shown as a measurable change extracellular acidificationrate. Moreover, culturing a third portion of the cells in the presenceof zsig63 polypeptide and the absence of a test compound can be used asa positive control for the zsig63-responsive cells, and as a control tocompare the agonist activity of a test compound with that of the zsig63polypeptide. Moreover, using the microphysiometer, there is provided amethod of identifying antagonists of zsig63 polypeptide, comprisingproviding cells responsive to a zsig63 polypeptide, culturing a firstportion of the cells in the presence of zsig63 and the absence of a testcompound, culturing a second portion of the cells in the presence ofzsig63 and the presence of a test compound, and detecting a change, forexample, an increase or a diminution in a cellular response of thesecond portion of the cells as compared to the first portion of thecells. The change in cellular response is shown as a measurable changeextracellular acidification rate. Antagonists and agonists, for zsig63polypeptide, can be rapidly identified using this method.

Moreover, zsig63 can be used to identify cells, tissues, or cell lineswhich respond to a zsig63-stimulated pathway. The microphysiometer,described above, can be used to rapidly identify ligand-responsivecells, such as cells responsive to zsig63 of the present invention.Cells can be cultured in the presence or absence of zsig63 polypeptide.Those cells which elicit a measurable change in extracellularacidification in the presence of zsig63 are responsive to zsig63. Suchcells, can be used to identify antagonists and agonists of zsig63polypeptide as described above.

zsig63 can also be used to identify inhibitors (antagonists) of itsactivity. Test compounds are added to the assays disclosed herein toidentify compounds that inhibit the activity of zsig63. In addition tothose assays disclosed herein, samples can be tested for inhibition ofzsig63 activity within a variety of assays designed to measure receptorbinding or the stimulation/inhibition of zsig63-dependent cellularresponses. For example, zsig63-responsive cell lines can be transfectedwith a reporter gene construct that is responsive to a zsig63-stimulatedcellular pathway. Reporter gene constructs of this type are known in theart, and will generally comprise a zsig63-DNA response element operablylinked to a gene encoding an assayable protein, such as luciferase. DNAresponse elements can include, but are not limited to, cyclic AMPresponse elements (CRE), hormone response elements (HRE) insulinresponse element (IRE) (Nasrin et al., Proc. Natl. Acad. Sci. USA87:5273-7, 1990) and serum response elements (SRE) (Shaw et al. Cell 56:563-72, 1989). Cyclic AMP response elements are reviewed in Roestler etal., J. Biol. Chem. 263 (19):9063-6; 1988 and Habener, Molec.Endocrinol. 4 (8):1087-94; 1990. Hormone response elements are reviewedin Beato, Cell 56:335-44; 1989. Candidate compounds, solutions, mixturesor extracts are tested for the ability to inhibit the activity of zsig63on the target cells as evidenced by a decrease in zsig63 stimulation ofreporter gene expression. Assays of this type will detect compounds thatdirectly block zsig63 binding to cell-surface receptors, as well ascompounds that block processes in the cellular pathway subsequent toreceptor-ligand binding. In the alternative, compounds or other samplescan be tested for direct blocking of zsig63 binding to receptor usingzsig63 tagged with a detectable label (e.g., ¹²⁵I, biotin, horseradishperoxidase, FITC, and the like). Within assays of this type, the abilityof a test sample to inhibit the binding of labeled zsig63 to thereceptor is indicative of inhibitory activity, which can be confirmedthrough secondary assays. Receptors used within binding assays may becellular receptors or isolated, immobilized receptors.

A zsig63 polypeptide can be expressed as a fusion with an immunoglobulinheavy chain constant region, typically an F_(c) fragment, which containstwo constant region domains and lacks the variable region. Methods forpreparing such fusions are disclosed in U.S. Pat. Nos. 5,155,027 and5,567,584. Such fusions are typically secreted as multimeric moleculeswherein the Fc portions are disulfide bonded to each other and twonon-Ig polypeptides are arrayed in closed proximity to each other.Fusions of this type can be used to affinity purify zsig63 receptor, asan in vitro assay tool, or as a zsig63 antagonist. For use in assays,the chimeras are bound to a support via the F_(c) region and used in anELISA format.

Zsig63 polypeptides can also be used to prepare antibodies that bind tozsig63 epitopes, peptides or polypeptides. The zsig63 polypeptide or afragment thereof serves as an antigen (immunogen) to inoculate an animaland elicit an immune response. One of skill in the art would recognizethat antigenic, epitope-bearing polypeptides contain a sequence of atleast 6, preferably at least 9, and more preferably at least 15 to about30 contiguous amino acid residues of a zsig63 polypeptide (e.g., SEQ IDNO:2). Polypeptides comprising a larger portion of a zsig63 polypeptide,i.e., from 30 to 10 residues up to the entire length of the amino acidsequence are included. Antigens or immunogenic epitopes can also includeattached tags, adjuvants and carriers, as described-herein. Suitableantigens include the zsig63 polypeptide encoded by SEQ ID NO:2 fromamino acid number 16 (Ala) to amino acid number 219 (Gln), or acontiguous 9 to 204 amino acid fragment thereof. Other suitable antigensinclude domains 1, 2, and 3, and the acidic motif and coil-like region,as disclosed herein. Preferred peptides to use as antigens arehydrophilic peptides such as those predicted by one of skill in the artfrom a hydrophobicity plot. Zsig63 hydrophilic peptides include peptidescomprising amino acid sequences selected from the group consisting of:amino acid residues 14 (Phe) to 19 (Arg) of SEQ ID NO:2; amino acidresidues 16 (Arg) to 21 (Phe) of SEQ ID NO:2; amino acid residues 24(Gly) to 29 (Asp) of SEQ ID NO:2; amino acid residues 25 (Glu) to 30(Asp) of SEQ ID NO:2; and amino acid residues 187Glu) to 192 (Glu) ofSEQ ID NO:2. Moreover, polypeptides that comprise hydrophilic epitopes,such as those predicted from a Jameson-Wolf profile, are preferredantigens, and include: amino acid residues 24 (Gly) to 33 (Pro) of SEQID NO:2; amino acid residues 17 (Lys) to 33 (Pro) of SEQ ID NO:2; aminoacid residues 66 (Thr) to 73 (Pro) of SEQ ID NO:2; amino acid residues103 (Pro) to 108 (Gly) of SEQ ID NO:2; amino acid residues 190 (Ala) to197 (Glu) of SEQ ID NO:2; amino acid residues 202 (Lys) to 215 (Gly) ofSEQ ID NO:2; and amino acid residues 190 (Ala) to 215 (Glu) of SEQ IDNO:2. Antibodies from an immune response generated by inoculation of ananimal with these antigens can be isolated and purified as describedherein. Methods for preparing and isolating polyclonal and monoclonalantibodies are well known in the art. See, for example, CurrentProtocols in Immunology, Cooligan, et al. (eds.), National Institutes ofHealth, John Wiley and Sons, Inc., 1995; Sambrook et al., MolecularCloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y.,1989; and Hurrell, J. G. R., Ed., Monoclonal Hybridoma Antibodies:Techniques and Applications, CRC Press, Inc., Boca Raton, Fla., 1982.

As would be evident to one of ordinary skill in the art, polyclonalantibodies can be generated from inoculating a variety of warm-bloodedanimals such as horses, cows, goats, sheep, dogs, chickens, rabbits,mice, and rats with a zsig63 polypeptide or a fragment thereof. Theimmunogenicity of a zsig63 polypeptide may be increased through the useof an adjuvant, such as alum (aluminum hydroxide) or Freund's completeor incomplete adjuvant. Polypeptides useful for immunization alsoinclude fusion polypeptides, such as fusions of zsig63 or a portionthereof with an immunoglobulin polypeptide or with maltose bindingprotein. The polypeptide immunogen may be a full-length molecule or aportion thereof. If the polypeptide portion is “hapten-like”, suchportion may be advantageously joined or linked to a macromolecularcarrier (such as keyhole limpet hemocyanin (KLH), bovine serum albumin(BSA) or tetanus toxoid) for immunization.

As used herein, the term “antibodies” includes polyclonal antibodies,affinity-purified polyclonal antibodies, monoclonal antibodies, andantigen-binding fragments, such as F(ab′)₂ and Fab proteolyticfragments. Genetically engineered intact antibodies or fragments, suchas chimeric antibodies, Fv fragments, single chain antibodies and thelike, as well as synthetic antigen-binding peptides and polypeptides,are also included. Non-human antibodies may be humanized by graftingnon-human CDRs onto human framework and constant regions, or byincorporating the entire non-human variable domains (optionally“cloaking” them with a human-like surface by replacement of exposedresidues, wherein the result is a “veneered” antibody). In someinstances, humanized antibodies may retain non-human residues within thehuman variable region framework domains to enhance proper bindingcharacteristics. Through humanizing antibodies, biological half-life maybe increased, and the potential for adverse immune reactions uponadministration to humans is reduced. Moreover, human antibodies can beproduced in transgenic, non-human animals that have been engineered tocontain human immunoglobulin genes as disclosed in WIPO Publication WO98/24893. It is preferred that the endogenous immunoglobulin genes inthese animals be inactivated or eliminated, such as by homologousrecombination.

Antibodies are considered to be specifically binding if: 1) they exhibita threshold level of binding activity, and 2) they do not significantlycross-react with related polypeptide molecules. A threshold level ofbinding is determined if anti-zsig63 antibodies herein bind to a zsig63polypeptide, peptide or epitope with an affinity at least 10-foldgreater than the binding affinity to control (non-zsig63) polypeptide.It is preferred that the antibodies exhibit a binding affinity (K_(a))of 10⁶ M⁻¹ or greater, preferably 10⁷ M⁻¹ or greater, more preferably10⁸ M⁻¹ or greater, and most preferably 10⁹ M⁻¹ or greater. The bindingaffinity of an antibody can be readily determined by one of ordinaryskill in the art, for example, by Scatchard analysis (Scatchard, G.,Ann. NY Acad. Sci. 51: 660-672, 1949).

Whether anti-zsig63 antibodies do not significantly cross-react withrelated polypeptide molecules is shown, for example, by the antibodydetecting zsig63 polypeptide but not known related polypeptides using astandard Western blot analysis (Ausubel et al., ibid.). Examples ofknown related polypeptides are those disclosed in the prior art, such asknown orthologs, and paralogs, and similar known members of a proteinfamily, Screening can also be done using non-human zsig63, and zsig63mutant polypeptides. Moreover, antibodies can be “screened against”known related polypeptides, to isolate a population that specificallybinds to the zsig63 polypeptides. For example, antibodies raised tozsig63 are adsorbed to related polypeptides adhered to insoluble matrix;antibodies specific to zsig63 will flow through the matrix under theproper buffer conditions. Screening allows isolation of polyclonal andmonoclonal antibodies non-crossreactive to known closely relatedpolypeptides (Antibodies: A Laboratory Manual, Harlow and Lane (eds.),Cold Spring Harbor Laboratory Press, 1988; Current Protocols inImmunology, Cooligan, et al. (eds.), National Institutes of Health, JohnWiley and Sons, Inc., 1995). Screening and isolation of specificantibodies is well known in the art. See, Fundamental Immunology, Paul(eds.), Raven Press, 1993; Getzoff et al., Adv. in Immunol. 43: 1-98,1988; Monoclonal Antibodies: Principles and Practice, Goding, J. W.(eds.), Academic Press Ltd., 1996; Benjamin et al., Ann. Rev. Immunol.2: 67-101, 1984. Specifically binding anti-zsig63 antibodies can bedetected by a number of methods in the art, and disclosed below.

A variety of assays known to those skilled in the art can be utilized todetect antibodies which bind to zsig63 proteins or polypeptides.Exemplary assays are described in detail in Antibodies: A LaboratoryManual, Harlow and Lane (Eds.), Cold Spring Harbor Laboratory Press,1988. Representative examples of such assays include: concurrentimmunoelectrophoresis, radioimmunoassay, radioimmuno-precipitation,enzyme-linked immunosorbent assay (ELISA), dot blot or Western blotassay, inhibition or competition assay, and sandwich assay. In addition,antibodies can be screened for binding to wild-type versus mutant zsig63protein or polypeptide.

Alternative techniques for generating or selecting antibodies usefulherein include in vitro exposure of lymphocytes to zsig63 protein orpeptide, and selection of antibody display libraries in phage or similarvectors (for instance, through use of immobilized or labeled zsig63protein or peptide). Genes encoding polypeptides having potential zsig63polypeptide binding domains can be obtained by screening random peptidelibraries displayed on phage (phage display) or on bacteria, such as E.coli. Nucleotide sequences encoding the polypeptides can be obtained ina number of ways, such as through random mutagenesis and randompolynucleotide synthesis. These random peptide display libraries can beused to screen for peptides which interact with a known target which canbe a protein or polypeptide, such as a ligand or receptor, a biologicalor synthetic macromolecule, or organic or inorganic substances.Techniques for creating and screening such random peptide displaylibraries are known in the art (Ladner et al., U.S. Pat. No. 5,223,409;Ladner et al., U.S. Pat. No. 4,946,778; Ladner et al., U.S. Pat. No.5,403,484 and Ladner et al., U.S. Pat. No. 5,571,698) and random peptidedisplay libraries and kits for screening such libraries are availablecommercially, for instance from Clontech (Palo Alto, Calif.), InvitrogenInc. (San Diego, Calif.), New England Biolabs, Inc. (Beverly, Mass.) andPharmacia LKB Biotechnology Inc. (Piscataway, N.J.). Random peptidedisplay libraries can be screened using the zsig63 sequences disclosedherein to identify proteins which bind to zsig63. These “bindingpolypeptides” which interact with zsig63 polypeptides can be used fortagging cells; for isolating homolog polypeptides by affinitypurification; they can be directly or indirectly conjugated to drugs,toxins, radionuclides and the like. These binding polypeptides can alsobe used in analytical methods such as for screening expression librariesand neutralizing activity, e.g., for blocking interaction between ligandand receptor, or viral binding to a receptor. The binding polypeptidescan also be used for diagnostic assays for determining circulatinglevels of zsig63 polypeptides; for detecting or quantitating solublezsig63 polypeptides as marker of underlying pathology or disease. Thesebinding polypeptides can also act as zsig63 antagonists to block zsig63binding and signal transduction in vitro and in vivo. These anti-zsig63binding polypeptides would be useful for inhibiting zsig63 activity orprotein-binding.

Antibodies to zsig63 may be used for tagging cells that express zsig63;for isolating zsig63 by affinity purification; for diagnostic assays fordetermining circulating levels of zsig63 polypeptides; for detecting orquantitating soluble zsig63 as marker of underlying pathology ordisease; in analytical methods employing FACS; for screening expressionlibraries; for generating anti-idiotypic antibodies; and as neutralizingantibodies or as antagonists to block zsig63 activity in vitro and invivo. Suitable direct tags or labels include radionuclides, enzymes,substrates, cofactors, inhibitors, fluorescent markers, chemiluminescentmarkers, magnetic particles and the like; indirect tags or labels mayfeature use of biotin-avidin or other complement/anti-complement pairsas intermediates. Antibodies herein may also be directly or indirectlyconjugated to drugs, toxins, radionuclides and the like, and theseconjugates used for in vivo diagnostic or therapeutic applications.Moreover, antibodies to zsig63 or fragments thereof may be used in vitroto detect denatured zsig63 or fragments thereof in assays, for example,Western Blots or other assays known in the art.

Molecules of the present invention can be used to identify and isolatereceptors for zsig63. For example, proteins and peptides of the presentinvention can be immobilized on a column and membrane preparations runover the column (Immobilized Affinity Ligand Techniques, Hermanson etal., eds., Academic Press, San Diego, Calif., 1992, pp.195-202).Proteins and peptides can also be radiolabeled (Methods in Enzymol.,vol. 182, “Guide to Protein Purification”, M. Deutscher, ed., Acad.Press, San Diego, 1990, 721-737) or photoaffinity labeled (Brunner etal., Ann. Rev. Biochem. 62:483-514, 1993 and Fedan et al., Biochem.Pharmacol. 33:1167-1180, 1984) and specific cell-surface proteins can beidentified.

Differentiation is a progressive and dynamic process, beginning withpluripotent stem cells and ending with terminally differentiated cells.Pluripotent stem cells that can regenerate without commitment to alineage express a set of differentiation markers that are lost whencommitment to a cell lineage is made. Progenitor cells express a set ofdifferentiation markers that may or may not continue to be expressed asthe cells progress down the cell lineage pathway toward maturation.Differentiation markers that are expressed exclusively by mature cellsare usually functional properties such as cell products, enzymes toproduce cell products, and receptors. The stage of a cell population'sdifferentiation is monitored by identification of markers present in thecell population. Myocytes, osteoblasts, adipocytes, chrondrocytes,fibroblasts and reticular cells are believed to originate from a commonmesenchymal stem cell (Owen et al., Ciba Fdn. Symp. 136:42-46, 1988).Markers for mesenchymal stem cells have not been well identified (Owenet al., J. of Cell Sci. 87:731-738, 1987), so identification is usuallymade at the progenitor and mature cell stages. The novel polypeptides ofthe present invention may be useful for studies to isolate mesenchymalstem cells and myocyte or other progenitor cells, both in vivo and exvivo.

There is evidence to suggest that factors that stimulate specific celltypes down a pathway towards terminal differentiation ordedifferentiation affect the entire cell population originating from acommon precursor or stem cell. Thus, the present invention includesstimulating or inhibiting the proliferation of myocytes, smooth musclecells, osteoblasts, adipocytes, chrondrocytes, neuronal and endothelialcells. Molecules of the present invention for example, may whilestimulating proliferation or differentiation of cardiac myocytes,inhibit proliferation or differentiation of adipocytes, by virtue of theaffect on their common precursor/stem cells. Thus molecules of thepresent invention may have use in inhibiting chondrosarcomas,atherosclerosis, restenosis and obesity.

Assays measuring differentiation include, for example, measuring cellmarkers associated with stage-specific expression of a tissue, enzymaticactivity, functional activity or morphological changes (Watt, FASEB,5:281-284, 1991; Francis, Differentiation 57:63-75, 1994; Raes, Adv.Anim. Cell Biol. Technol. Bioprocesses, 161-171, 1989; all incorporatedherein by reference). Alternatively, zsig63 polypeptide itself can serveas an additional cell-surface or secreted marker associated withstage-specific expression of a tissue. As such, direct measurement ofzsig63 polypeptide, or its loss of expression in a tissue as itdifferentiates, can serve as a marker for differentiation of tissues.

Similarly, direct measurement of zsig63 polypeptide, or its loss ofexpression in a tissue can be determined in a tissue or cells as theyundergo tumor progression. Increases in invasiveness and motility ofcells, or the gain or loss of expression of zsig63 in a pre-cancerous orcancerous condition, in comparison to normal tissue, can serve as adiagnostic for transformation, invasion and metastasis in tumorprogression. As such, knowledge of a tumor's stage of progression ormetastasis will aid the physician in choosing the most proper therapy,or aggressiveness of treatment, for a given individual cancer patient.Methods of measuring gain and loss of expression (of either mRNA orprotein) are well known in the art and described herein and can beapplied to zsig63 expression. For example, appearance or disappearanceof polypeptides that regulate cell motility can be used to aid diagnosisand prognosis of prostate cancer (Banyard, J. and Zetter, B. R., Cancerand Metast. Rev. 17:449-458, 1999). As an effector of cell motility,zsig63 gain or loss of expression may serve as a diagnostic for prostateand other cancers.

Moreover, the activity and effect of zsig63 on tumor progression andmetastasis can be measured in vivo. Several syngeneic mouse models havebeen developed to study the influence of polypeptides, compounds orother treatments on tumor progression. In these models, tumor cellspassaged in culture are implanted into mice of the same strain as thetumor donor. The cells will develop into tumors having similarcharacteristics in the recipient mice, and metastasis will also occur insome of the models. Appropriate tumor models for our studies include theLewis lung carcinoma (ATCC No. CRL-1642) and B16 melanoma (ATCC No.CRL-6323), amongst others. These are both commonly used tumor lines,syngeneic to the C57BL6 mouse, that are readily cultured and manipulatedin vitro. Tumors resulting from implantation of either of these celllines are capable of metastasis to the lung in C57BL6 mice. The Lewislung carcinoma model has recently been used in mice to identify aninhibitor of angiogenesis (O'Reilly M S, et al. Cell 79: 315-328,1994).C57BL6/J. mice are treated with an experimental agent either throughdaily injection of recombinant protein, agonist or antagonist or a onetime injection of recombinant adenovirus. Three days following thistreatment, 10⁵ to 10⁶ cells are implanted under the dorsal skin.Alternatively, the cells themselves may be infected with recombinantadenovirus, such as one expressing zsig63, before implantation so thatthe protein is synthesized at the tumor site or intracellularly, ratherthan systemically.

The mice normally develop visible tumors within 5 days. The tumors areallowed to grow for a period of up to 3 weeks, during which time theymay reach a size of 1500-1800 mm³ in the control treated group. Tumorsize and body weight are carefully monitored throughout the experiment.At the time of sacrifice, the tumor is removed and weighed along withthe lungs and the liver. The lung weight has been shown to correlatewell with metastatic tumor burden. As an additional measure, lungsurface metastases are counted. The resected tumor, lungs and liver areprepared for histopathological examination, immunohistochemistry, and insitu hybridization, using methods known in the art and described herein.The influence of the expressed polypeptide in question, e.g., zsig63, onthe ability of the tumor to recruit vasculature and undergo metastasiscan thus be assessed. In addition, aside from using adenovirus, theimplanted cells can be transiently transfected with zsig63. Use ofstable zsig63 transfectants as well as use of induceable promoters toactivate zsig63 expression in vivo are known in the art and can be usedin this system to assess zsig63 induction of metastasis. Moreover,purified zsig63 or zsig63 conditioned media can be directly injected into this mouse model, and hence be used in this system. For generalreference see, O'Reilly M S, et al. Cell 79:315-328, 1994; and RuscianoD, et al. Murine Models of Liver Metastasis. Invasion Metastasis14:349-361, 1995.

The activity of zsig63 and its derivatives (conjugates) on growth anddissemination of tumor cells derived from human hematologic malignanciescan also be measured in vivo in a mouse Xenograft model Several mousemodels have been developed in which human tumor cells are implanted intoimmunodeficient mice, collectively referred to as xenograft models. SeeCattan, A R and Douglas, E Leuk. Res. 18:513-22, 1994; and Flavell, D J,Hematological Oncology 14:67-82, 1996. The characteristics of thedisease model vary with the type and quantity of cells delivered to themouse. Typically, the tumor cells will proliferate rapidly and can befound circulating in the blood and populating numerous organ systems.Therapeutic strategies appropriate for testing in such a model includeantibody induced toxicity, ligand-toxin conjugates or cell-basedtherapies. The latter method, commonly referred to adoptiveimmunotherapy, involves treatment of the animal with components of thehuman immune system (i.e. lymphocytes, NK cells) and may include ex vivoincubation of cells with zsig63 or other immunomodulatory agents.

Polynucleotides encoding zsig63 polypeptides are useful within genetherapy applications where it is desired to increase or inhibit zsig63activity. If a mammal has a mutated or absent zsig63 gene, the zsig63gene can be introduced into the cells of the mammal. In one embodiment,a gene encoding a zsig63 polypeptide is introduced in vivo in a viralvector. Such vectors include an attenuated or defective DNA virus, suchas, but not limited to, herpes simplex virus (HSV), papillomavirus,Epstein Barr virus (EBV), adenovirus, adeno-associated virus (AAV), andthe like. Defective viruses, which entirely or almost entirely lackviral genes, are preferred. A defective virus is not infective afterintroduction into a cell. Use of defective viral vectors allows foradministration to cells in a specific, localized area, without concernthat the vector can infect other cells. Examples of particular vectorsinclude, but are not limited to, a defective herpes simplex virus 1(HSV1) vector (Kaplitt et al., Molec. Cell. Neurosci. 2:320-30, 1991);an attenuated adenovirus vector, such as the vector described byStratford-Perricaudet et al., J. Clin. Invest. 90:626-30, 1992; and adefective adeno-associated virus vector (Samulski et al., J. Virol.61:3096-101, 1987; Samulski et al., J. Virol. 63:3822-8, 1989).

In another embodiment, a zsig63 gene can be introduced in a retroviralvector, e.g., as described in Anderson et al., U.S. Pat. No. 5,399,346;Mann et al. Cell 33:153, 1983; Temin et al., U.S. Pat. No. 4,650,764;Temin et al., U.S. Pat. No. 4,980,289; Markowitz et al., J. Virol.62:1120, 1988; Temin et al., U.S. Pat. No. 5,124,263; InternationalPatent Publication No. WO 95/07358, published Mar. 16, 1995 by Doughertyet al.; and Kuo et al., Blood 82:845, 1993. Alternatively, the vectorcan be introduced by lipofection in vivo using liposomes. Syntheticcationic lipids can be used to prepar liposomes for in vivo transfectionof a gene encoding a marker (Felgner et al., Proc. Natl. Acad. Sci. USA84:7413-7, 1987; Mackey et al., Proc. Natl. Acad. Sci. USA 85:8027-31,1988). The use of lipofection to introduce exogenous genes into specificorgans in vivo has certain practical advantages. Molecular targeting ofliposomes to specific cells represents one area of benefit. Moreparticularly, directing transfection to particular cells represents onearea of benefit. For instance, directing transfection to particular celltypes would be particularly advantageous in a tissue with cellularheterogeneity, such as the pancreas, liver, kidney, and brain. Lipidsmay be chemically coupled to other molecules for the purpose oftargeting. Targeted peptides (e.g., hormones or neurotransmitters),proteins such as antibodies, or non-peptide molecules can be coupled toliposomes chemically.

It is possible to remove the target cells from the body; to introducethe vector as a naked DNA plasmid; and then to re-implant thetransformed cells into the body. Naked DNA vectors for gene therapy canbe introduced into the desired host cells by methods known in the art,e.g., transfection, electroporation, microinjection, transduction, cellfusion, DEAE dextran, calcium phosphate precipitation, use of a gene gunor use of a DNA vector transporter. See, e.g., Wu et al., J. Biol. Chem.267:963-7, 1992; Wu et al., J. Biol. Chem. 263:14621-4, 1988.

Antisense methodology can be used to inhibit zsig63 gene transcription,such as to inhibit cell proliferation in vivo. Polynucleotides that arecomplementary to a segment of a zsig63-encoding polynucleotide (e.g., apolynucleotide as set forth in SEQ ID NO:1) are designed to bind tozsig63-encoding mRNA and to inhibit translation of such mRNA. Suchantisense polynucleotides are used to inhibit expression of zsig63polypeptide-encoding genes in cell culture or in a subject.

Polynucleotides of the present invention are also used to detectabnormalities on human chromosome 4 associated with disease or otherhuman traits. The polynucleotides of the present invention map to the4q12-4q13region on human chromosome 4. Zsig63 maps 3.15 cR_(—)3000 fromthe framework marker WI-7844 on the chromosome 4 WICGR radiation hybridmap. Proximal and distal framework markers were WI-7844 and WI-4767,respectively. The use of surrounding markers positions zsig63 in the4q12-4q13 region on the integrated LDB chromosome 4 map. (see Example3).

The present invention also provides reagents which will find use indiagnostic applications. For example, the zsig63 gene, a probecomprising zsig63 DNA or RNA or a subsequence thereof can be used todetermine if the zsig63 gene is present on chromosome 4 or if a mutationhas occurred. Detectable chromosomal aberrations at the zsig63 genelocus include but are not limited to aneuploidy, gene copy numberchanges, insertions, deletions, translocations, restriction site changesand rearrangements. Such aberrations can be detected usingpolynucleotides of the present invention by employing molecular genetictechniques, such as restriction fragment length polymorphism (RFLP)analysis, short tandem repeat (STR) analysis employing PCR techniques,and other genetic linkage analysis techniques known in the art (Sambrooket al., ibid.; Ausubel, et. al., ibid.; Marian, A. J., Chest, 108:255-265, 1995). These methods can be employed to use zsig63polynucleotides to detect abnormalities on human chromosome 4, such asthose described below.

The precise knowledge of a gene's position can be useful for a number ofpurposes, including: 1) determining if a sequence is part of an existingcontig and obtaining additional surrounding genetic sequences in variousforms, such as YACs, BACs or cDNA clones; 2) providing a possiblecandidate gene for an inheritable disease which shows linkage to thesame chromosomal region; and 3) cross-referencing model organisms, suchas mouse, which may aid in determining what function a particular genehas.

Zsig63 is located at the 4q12-4q13 region of chromosome 4. Several genesof known function map to this region. Zsig63 polynucleotide probes canbe used to detect abnormalities or genotypes associated with thesedefects. There are several genes that map to the zsig63 locus that areassociated with human disease states, such as dental diseases: Forexample, Dentinogenesis imperfecta (4q13-q21) and dentin dysplasia, typeII (4q) map near zsig63. As a salivary protein that also maps to thisregion of chromosome 4, defects in zsig63 may also play a role in dentaldisease, such as causing a defect in dental formation; and/orpredisposition to dental carries and periodontal disease, as the salivais important in maintaining a healthy microbial environment in themouth. Moreover, a v-kit oncogene homolog related to Piebaldism andcertain severe malignancies (e.g., certain leukemias) maps to 4q12 andis involved in common malignant gastrointestinal stromal tumors (GIST)tumors. As zsig63 maps to 4q12-q13 as well, there can be an associationbetween loss of zsig63 function and tumor formation or progression.Moreover, translocations and duplications in 4q12 are seen in v-kitoncogene homolog related diseases. Thus, zsig63 polynucleotide probescan be used to detect abnormalities or genotypes associated with thesediseases cancer susceptibility markers, as well as detection ofchromosome translocations associated therewith. Because there isabundant evidence for cancer resulting from mutations in the 4q12region, and zsig63 also maps to this chromosomal locus, mutations inzsig63 may also be directly involved in or associated with cancers, suchas lymphoid cell cancers, gastrointestinal and salivary gland tumors,solid tumors or other tumors.

A diagnostic could assist physicians in determining the type of diseaseand appropriate associated therapy, or assistance in genetic counseling.As such, the inventive anti-zsig63 antibodies, polynucleotides, andpolypeptides can be used for the detection of zsig63 polypeptide, mRNAor anti-zsig63 antibodies, thus serving as markers and be directly usedfor detecting or genetic diseases or cancers, as described herein, usingmethods known in the art and described herein. Further, zsig63polynucleotide probes can be used to detect abnormalities or genotypesassociated with chromosome 4q12-q13 deletions and translocationsassociated with human diseases, such as those described above, or othertranslocations involved with malignant progression of tumors or other4q12-q13 mutations, which are expected to be involved in chromosomerearrangements in malignancy; or in other cancers. Similarly, zsig63polynucleotide probes can be used to detect abnormalities or genotypesassociated with chromosome 4q12-q13 trisomy and chromosome lossassociated with human diseases or spontaneous abortion. Moreover,amongst other genetic loci, those for Sarcoglycan linked musculardystrophy (4q12), Stargardt Disease (4q), and others, all manifestthemselves in human disease states as well as map to this region of thehuman genome. See the Online Mendellian Inheritance of Man (OMIM) genemap, and references therein, for this region of chromosome 4 on apublicly available WWW server(http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/getmap?chromosome=4q12).All of these serve as possible candidate genes for an inheritabledisease which show linkage to the same chromosomal region as the zsig63gene. Thus, zsig63 polynucleotide probes can be used to detectabnormalities or genotypes associated with these defects.

A diagnostic could assist physicians in determining the type of diseaseand appropriate associated therapy, or assistance in genetic counseling.As such, the inventive anti-zsig63 antibodies, polynucleotides, andpolypeptides can be used for the detection of zsig63 polypeptide, mRNAor anti-zsig63 antibodies, thus serving as markers and be directly usedfor detecting or genetic diseases or cancers, as described herein, usingmethods known in the art and described herein. Further, zsig63polynucleotide probes can be used to detect abnormalities or genotypesassociated with chromosome 4q12-q13 deletions and translocationsassociated with human diseases, or other translocations involved withmalignant progression of tumors or other 4q12-q13 mutations, which areexpected to be involved in chromosome rearrangements in malignancy; orin other cancers. Similarly, zsig63 polynucleotide probes can be used todetect abnormalities or genotypes associated with chromosome 4q12-q13trisomy and chromosome loss associated with human diseases orspontaneous abortion. Thus, zsig63 polynucleotide probes can be used todetect abnormalities or genotypes associated with these defects.

Similarly, defects in the zsig63 gene itself may result in a heritablehuman disease state. Molecules of the present invention, such as thepolypeptides, antagonists, agonists, polynucleotides and antibodies ofthe present invention would aid in the detection, diagnosis prevention,and treatment associated with a zsig63 genetic defect. As discussedabove, defects in the zsig63 gene itself may result in a heritable humandisease state or increase susceptibility to certain diseases.

Molecules of the present invention, such as the polypeptides,antagonists, agonists, polynucleotides and antibodies of the presentinvention would aid in the detection, diagnosis prevention, andtreatment associated with a zsig63 genetic defect. In addition, zsig63polynucleotide probes can be used to detect allelic differences betweendiseased or non-diseased individuals at the zsig63 chromosomal locus. Assuch, the zsig63 sequences can be used as diagnostics in forensic DNAprofiling.

In general, the diagnostic methods used in genetic linkage analysis, todetect a genetic abnormality or aberration in a patient, are known inthe art. Most diagnostic methods comprise the steps of (a) obtaining agenetic sample from a potentially diseased patient, diseased patient orpotential non-diseased carrier of a recessive disease allele; (b)producing a first reaction product by incubating the genetic sample witha zsig63 polynucleotide probe wherein the polynucleotide will hybridizeto complementary polynucleotide sequence, such as in RFLP analysis or byincubating the genetic sample with sense and antisense primers in a PCRreaction under appropriate PCR reaction conditions; (iii) Visualizingthe first reaction product by gel electrophoresis and/or other knownmethod such as visualizing the first reaction product with a zsig63polynucleotide probe wherein the polynucleotide will hybridize to thecomplementary polynucleotide sequence of the first reaction; and (iv)comparing the visualized first reaction product to a second controlreaction product of a genetic sample from wild type patient. Adifference between the first reaction product and the control reactionproduct is indicative of a genetic abnormality in the diseased orpotentially diseased patient, or the presence of a heterozygousrecessive carrier phenotype for a non-diseased patient, or the presenceof a genetic defect in a tumor from a diseased patient, or the presenceof a genetic abnormality in a fetus or pre-implantation embryo. Forexample, a difference in restriction fragment pattern, length of PCRproducts, length of repetitive sequences at the zsig63 genetic locus,and the like, are indicative of a genetic abnormality, geneticaberration, or allelic difference in comparison to the normal wild typecontrol. Controls can be from unaffected family members, or unrelatedindividuals, depending on the test and availability of samples. Geneticsamples for use within the present invention include genomic DNA, mRNA,and cDNA isolated form any tissue or other biological sample from apatient, such as but not limited to, blood, saliva, semen, embryoniccells, amniotic fluid, and the like. The polynucleotide probe or primercan be RNA or DNA, and will comprise a portion of SEQ ID NO:1, thecomplement of SEQ ID NO:1, or an RNA equivalent thereof. Such methods ofshowing genetic linkage analysis to human disease phenotypes are wellknown in the art. For reference to PCR based methods in diagnostics seesee, generally, Mathew (ed.), Protocols in Human Molecular Genetics(Humana Press, Inc. 1991), White (ed.), PCR Protocols: Current Methodsand Applications (Humana Press, Inc. 1993), Cotter (ed.), MolecularDiagnosis of Cancer (Humana Press, Inc. 1996), Hanausek and Walaszek(eds.), Tumor Marker Protocols (Humana Press, Inc. 1998), Lo (ed.),Clinical Applications of PCR (Humana Press, Inc. 1998), and Meltzer(ed.), PCR in Bioanalysis (Humana Press, Inc. 1998)).

Mutations associated with the zsig63 locus can be detected using nucleicacid molecules of the present invention by employing standard methodsfor direct mutation analysis, such as restriction fragment lengthpolymorphism analysis, short tandem repeat analysis employing PCRtechniques, amplification-refractory mutation system analysis,single-strand conformation polymorphism detection, RNase cleavagemethods, denaturing gradient gel electrophoresis, fluorescence-assistedmismatch analysis, and other genetic analysis techniques known in theart (see, for example, Mathew (ed.), Protocols in Human MolecularGenetics (Humana Press, Inc. 1991), Marian, Chest 108:255 (1995),Coleman and Tsongalis, Molecular Diagnostics (Human Press, Inc. 1996),Elles (ed.) Molecular Diagnosis of Genetic Diseases (Humana Press, Inc.1996), Landegren (ed.), Laboratory Protocols for Mutation Detection(Oxford University Press 1996), Birren et al. (eds.), Genome Analysis,Vol. 2: Detecting Genes (Cold Spring Harbor Laboratory Press 1998),Dracopoli et al. (eds.), Current Protocols in Human Genetics (John Wiley& Sons 1998), and Richards and Ward, “Molecular Diagnostic Testing,” inPrinciples of Molecular Medicine, pages 83-88 (Humana Press, Inc.1998)). Direct analysis of an zsig63 gene for a mutation can beperformed using a subject's genomic DNA. Methods for amplifying genomicDNA, obtained for example from peripheral blood lymphocytes, arewell-known to those of skill in the art (see, for example, Dracopoli etal. (eds.), Current Protocols in Human Genetics, at pages 7.1.6 to 7.1.7(John Wiley & Sons 1998)).

Mice engineered to express the zsig63 gene, referred to as “transgenicmice,” and mice that exhibit a complete absence of zsig63 gene function,referred to as “knockout mice,” may also be generated (Snouwaert et al.,Science 257:1083, 1992; Lowell et al., Nature 366:740-42, 1993;Capecchi, M. R., Science 244: 1288-1292, 1989; Palmiter, R. D. et al.Annu Rev Genet. 20: 465-499, 1986). For example, transgenic mice thatover-express zsig63, either ubiquitously or under a tissue-specific ortissue-restricted promoter can be used to ask whether over-expressioncauses a phenotype. For example, over-expression of a wild-type zsig63polypeptide, polypeptide fragment or a mutant thereof may alter normalcellular processes, resulting in a phenotype that identifies a tissue inwhich zsig63 expression is functionally relevant and may indicate atherapeutic target for the zsig63, its agonists or antagonists. Forexample, a preferred transgenic mouse to engineer is one thatover-expresses the zsig63 mature polypeptide (approximately amino acids16 (Ala) to 219 (Gln) of SEQ ID NO:2). Moreover, such over-expressionmay result in a phenotype that shows similarity with human diseases.Similarly, knockout zsig63 mice can be used to determine where zsig63 isabsolutely required in vivo. The phenotype of knockout mice ispredictive of the in vivo effects of that a zsig63 antagonist, such asthose described herein, may have. The human zsig63 cDNA can be used toisolate murine zsig63 mRNA, cDNA and genomic DNA, which are subsequentlyused to generate knockout mice. These mice may be employed to study thezsig63 gene and the protein encoded thereby in an in vivo system, andcan be used as in vivo models for corresponding human diseases.Moreover, transgenic mice expression of zsig63 antisense polynucleotidesor ribozymes directed against zsig63, described herein, can be usedanalogously to transgenic mice described above.

For pharmaceutical use, the proteins of the present invention areformulated for topical, inhalant or parenteral, particularly intravenousor subcutaneous, delivery according to conventional methods. Intravenousadministration will be by bolus injection or infusion over a typicalperiod of one to several hours. In general, pharmaceutical formulationswill include a zsig63 protein in combination with a pharmaceuticallyacceptable vehicle, such as saline, buffered saline, 5% dextrose inwater or the like. Formulations may further include one or moreexcipients, preservatives, solubilizers, buffering agents, albumin toprevent protein loss on vial surfaces, etc. Methods of formulation arewell known in the art and are disclosed, for example, in Remington: TheScience and Practice of Pharmacy, Gennaro, ed., Mack Publishing Co.,Easton, Pa., 19th ed., 1995. Therapeutic doses will generally determinedby the clinician according to accepted standards, taking into accountthe nature and severity of the condition to be treated, patient traits,etc. Determination of dose is within the level of ordinary skill in theart. The proteins may be administered for acute treatment, over one weekor less, often over a period of one to three days or may be used inchronic treatment, over several months or years.

The invention is further illustrated by the following non-limitingexamples.

EXAMPLE 1 Identification of zsig63 Using an EST Sequence to ObtainFull-length zsig63

Scanning of a translated DNA database resulted in identification of anexpressed sequence tag (EST) sequence found to be a novel member of theadhesin family and designated zsig63.

Confirmation of the EST sequence was made by sequence analyses of thecDNA from which the EST originated. This cDNA clone was obtained andsequenced using the following primers: ZC6768 (SEQ ID NO:4), ZC694 (SEQID NO:5), ZC7231 (SEQ ID NO:6), ZC7764a (SEQ ID NO:7). The insert wasabout 1 kb and was full-length.

EXAMPLE 2 Tissue Distribution

Northern blot analysis was performed using Human Multiple TissueNorthern™ Blots (MTN I, MTN II, MTN III) (Clontech) and an in-houseNorthern blot prepared using 2 mg each of human testis, prostate spinalcord, salivary gland, thymus, and thyroid poly-A+ RNA (Clontech). Theplasmid containing full-length zsig63 (Example 1) was digested as permanufacturer's instructions with HindIII and XbaI (New England BioLabs,Beverly, Mass.) for 2 hours at 37° C. A sample of the digested plasmidDNA was run on a 1% agarose gel. A band of the expected size of 662 bpwas seen. The 662 bp fragment, was gel purified using a commerciallyavailable kit (QiaexII™; Qiagen) and then radioactively labeled with³²P-dCTP using Rediprime II™ (Amersham), a random prime labeling system,according to the manufacturer's specifications. The probe was thenpurified using a Nuc-Trap™ column (Stratagene) according to themanufacturer's instructions. ExpressHyb™ (Clontech) solution was usedfor prehybridization and as a hybridizing solution for the Northernblots. Hybridization took place overnight at 65° C. using 1-2×10⁶ cpm/mlof labeled probe. The blots were then washed 4 times for 20 minutes in2×SSC/0.1% SDS at 25° C., and then twice more in 0.1×SSC/0.1% SDS at 50°C. for 30 minutes each. A transcript of approximately 1.3 kb wasdetected at very high levels in salivary gland, and moderate to lowlevels in thyroid and prostate.

Dot Blots were also performed using Human RNA Master Blots™ (Clontech).The methods and conditions for the Dot Blots are the same as for theMultiple Tissue Blots described above. Dot blot had a very strong signalin salivary gland.

EXAMPLE 3 Chromosomal Mapping of the zsig63 Gene

Zsig63 was mapped to chromosome 4 using the commercially available“GeneBridge 4 Radiation Hybrid Panel” (Research Genetics, Inc.,Huntsville, Ala.). The GeneBridge 4 Radiation Hybrid Panel contains DNAsfrom each of 93 radiation hybrid clones, plus two control DNAs (the HFLdonor and the A23 recipient). A publicly available WWW server(http://www-genome.wi.mit.edu/cgi-bin/contig/rhmapper.pl) allows mappingrelative to the Whitehead Institute/MIT Center for Genome Research'sradiation hybrid map of the human genome (the “WICGR” radiation hybridmap) which was constructed with the GeneBridge 4 Radiation Hybrid Panel.

For the mapping of zsig63 with the “GeneBridge 4 RH Panel”, 20 μlreactions were set up in a 96-well microtiter plate (Stratagene, LaJolla, Calif.) and used in a “RoboCycler Gradient 96” thermal cycler(Stratagene). Each of the 95 PCR reactions consisted of 2 μl 10× KlenTaqPCR reaction buffer (Clontech Laboratories, Inc., Palo Alto, Calif.),1.6 μl dNTPs mix (2.5 mM each, Perkin-Elmer, Foster City, Calif.), 1 μlsense primer, ZC 20,555, (SEQ ID NO:8) 1 μl antisense primer, ZC 20,556,(SEQ ID NO:9) 2 μl “RediLoad” (Research Genetics, Inc., Huntsville,Ala.), 0.4 μl 50× Advantage KlenTaq Polymerase Mix (Clontech), 25 ng ofDNA from an individual hybrid clone or control and ddH₂O for a totalvolume of 20 μl. The reactions were overlaid with an equal amount ofmineral oil and sealed. The PCR cycler conditions were as follows: aninitial 1 cycle 5 minute denaturation at 94° C., 35 cycles of a 45seconds denaturation at 94° C., 45 seconds annealing at 58° C. and 1minute and 15 seconds extension at 72° C., followed by a final 1 cycleextension of 7 minutes at 72° C. The reactions were separated byelectrophoresis on a 2% agarose gel (Life Technologies, Gaithersburg,Md.).

The results showed that zsig63 maps 3.15 cR_(—)3000 from the frameworkmarker WI-7844 on the chromosome 4 WICGR radiation hybrid map. Proximaland distal framework markers were WI-7844 and WI-4767, respectively. Theuse of surrounding markers positions zsig63 in the 4q12-4q13 region onthe integrated LDB chromosome 4 map (The Genetic Location Database,University of Southhampton, WWW server: http://cedar.genetics.soton.ac.uk/public_html/).

From the foregoing, it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims.

9 1 1008 DNA Homo sapiens CDS (128)...(784) 1 agacagacta aaaaagccatgtattctttc gtttctctct aaaagaagaa aaatataatt 60 taaaaataca ttgcgtattttctaaaacaa taaatttata gtgttaatat tcatagggtc 120 aatcaaa atg aag ctt ctcctt tgg gcc tgc att gta tgt gtt gct ttt 169 Met Lys Leu Leu Leu Trp AlaCys Ile Val Cys Val Ala Phe 1 5 10 gca agg aag aga cgg ttc ccc ttc attggt gag gat gac aat gac gat 217 Ala Arg Lys Arg Arg Phe Pro Phe Ile GlyGlu Asp Asp Asn Asp Asp 15 20 25 30 ggt cac cca ctt cat cca tct ctg aatatt cct tat ggc ata cgg aat 265 Gly His Pro Leu His Pro Ser Leu Asn IlePro Tyr Gly Ile Arg Asn 35 40 45 tta cca cct cct ctt tat tat cgc cca gtgaat aca gtc ccc agt tac 313 Leu Pro Pro Pro Leu Tyr Tyr Arg Pro Val AsnThr Val Pro Ser Tyr 50 55 60 cct ggg aat act tac act gac aca ggg tta ccttcg tat ccc tgg att 361 Pro Gly Asn Thr Tyr Thr Asp Thr Gly Leu Pro SerTyr Pro Trp Ile 65 70 75 cta act tct cct gga ttc ccc tat gtc tat cac atccgt ggt ttt ccc 409 Leu Thr Ser Pro Gly Phe Pro Tyr Val Tyr His Ile ArgGly Phe Pro 80 85 90 tta gct act cag ttg aat gtt cct cct ctc cct cct aggggt ttc ccg 457 Leu Ala Thr Gln Leu Asn Val Pro Pro Leu Pro Pro Arg GlyPhe Pro 95 100 105 110 ttt gtc cct cct tca agg ttt ttt tca gca gct gcagca ccc gct gcc 505 Phe Val Pro Pro Ser Arg Phe Phe Ser Ala Ala Ala AlaPro Ala Ala 115 120 125 cca cct att gca gct gag cct gct gca gct gca cctctt aca gcc aca 553 Pro Pro Ile Ala Ala Glu Pro Ala Ala Ala Ala Pro LeuThr Ala Thr 130 135 140 cct gta gca gct gag cct gct gca ggg gcc cct gttgca gct gag cct 601 Pro Val Ala Ala Glu Pro Ala Ala Gly Ala Pro Val AlaAla Glu Pro 145 150 155 gct gca gag gca cct gtt gga gct gag cct gct gcagag gca cct gtt 649 Ala Ala Glu Ala Pro Val Gly Ala Glu Pro Ala Ala GluAla Pro Val 160 165 170 gca gct gag cct gct gca gag gca cct gtt gga gtggag cca gct gca 697 Ala Ala Glu Pro Ala Ala Glu Ala Pro Val Gly Val GluPro Ala Ala 175 180 185 190 gag gaa cct tca cca gct gag cct gct aca gccaag cct gct gcc cca 745 Glu Glu Pro Ser Pro Ala Glu Pro Ala Thr Ala LysPro Ala Ala Pro 195 200 205 gaa cct cac cct tct ccc tct ctt gaa cag gcaaat cag tgaaattctc 794 Glu Pro His Pro Ser Pro Ser Leu Glu Gln Ala AsnGln 210 215 tagaagagta ccatgggttc atttctatac tgatgcagaa ataagtgaaatctacaaaag 854 ttttctttct tttccaaaga ctatttcatt ctgttgtatt cagagtattcatctcactac 914 attgatttgt ttgtggtagt ttttccttgg acttaattta tattgaaaaaacattgataa 974 ttaaataaat aaaatagata atttagacca atgg 1008 2 219 PRT Homosapiens 2 Met Lys Leu Leu Leu Trp Ala Cys Ile Val Cys Val Ala Phe AlaArg 1 5 10 15 Lys Arg Arg Phe Pro Phe Ile Gly Glu Asp Asp Asn Asp AspGly His 20 25 30 Pro Leu His Pro Ser Leu Asn Ile Pro Tyr Gly Ile Arg AsnLeu Pro 35 40 45 Pro Pro Leu Tyr Tyr Arg Pro Val Asn Thr Val Pro Ser TyrPro Gly 50 55 60 Asn Thr Tyr Thr Asp Thr Gly Leu Pro Ser Tyr Pro Trp IleLeu Thr 65 70 75 80 Ser Pro Gly Phe Pro Tyr Val Tyr His Ile Arg Gly PhePro Leu Ala 85 90 95 Thr Gln Leu Asn Val Pro Pro Leu Pro Pro Arg Gly PhePro Phe Val 100 105 110 Pro Pro Ser Arg Phe Phe Ser Ala Ala Ala Ala ProAla Ala Pro Pro 115 120 125 Ile Ala Ala Glu Pro Ala Ala Ala Ala Pro LeuThr Ala Thr Pro Val 130 135 140 Ala Ala Glu Pro Ala Ala Gly Ala Pro ValAla Ala Glu Pro Ala Ala 145 150 155 160 Glu Ala Pro Val Gly Ala Glu ProAla Ala Glu Ala Pro Val Ala Ala 165 170 175 Glu Pro Ala Ala Glu Ala ProVal Gly Val Glu Pro Ala Ala Glu Glu 180 185 190 Pro Ser Pro Ala Glu ProAla Thr Ala Lys Pro Ala Ala Pro Glu Pro 195 200 205 His Pro Ser Pro SerLeu Glu Gln Ala Asn Gln 210 215 3 657 DNA Artificial Sequence Degeneratepolynucleotide sequence for zsig63 3 atgaarytny tnytntgggc ntgyathgtntgygtngcnt tygcnmgnaa rmgnmgntty 60 ccnttyathg gngargayga yaaygaygayggncayccny tncayccnws nytnaayath 120 ccntayggna thmgnaayyt nccnccnccnytntaytaym gnccngtnaa yacngtnccn 180 wsntayccng gnaayacnta yacngayacnggnytnccnw sntayccntg gathytnacn 240 wsnccnggnt tyccntaygt ntaycayathmgnggnttyc cnytngcnac ncarytnaay 300 gtnccnccny tnccnccnmg nggnttyccnttygtnccnc cnwsnmgntt yttywsngcn 360 gcngcngcnc cngcngcncc nccnathgcngcngarccng cngcngcngc nccnytnacn 420 gcnacnccng tngcngcnga rccngcngcnggngcnccng tngcngcnga rccngcngcn 480 gargcnccng tnggngcnga rccngcngcngargcnccng tngcngcnga rccngcngcn 540 gargcnccng tnggngtnga rccngcngcngargarccnw snccngcnga rccngcnacn 600 gcnaarccng cngcnccnga rccncayccnwsnccnwsny tngarcargc naaycar 657 4 25 DNA Artificial SequenceOligonucleotide primer ZC6768 4 gcaattaacc ctcactaaag ggaac 25 5 20 DNAArtificial Sequence Oligonucleotide primer ZC694 5 taatacgact cactataggg20 6 26 DNA Artificial Sequence Oligonucleotide primer ZC7231 6tttttttttt tttttttttt tttttv 26 7 26 DNA Artificial SequenceOligonucleotide primer ZC7764a 7 tttttttttt tttttttttt ttttta 26 8 18DNA Artificial Sequence Oligonucleotide primer ZC20555 8 ccacctcctctttattat 18 9 18 DNA Artificial Sequence Oligonucleotide primer ZC205569 aatccaggag aagttaga 18

What is claimed is:
 1. A fusion protein produced by a method comprising:culturing a host cell into which has been introduced a vector comprisingthe following operably linked elements: (a) a transcriptional promoter;(b) a DNA construct encoding a fusion protein, the DNA constructcomprising: a first DNA segment encoding a polypeptide selected from thegroup consisting of: (i) the amino acid sequence of SEQ ID NO: 2 fromresidue number 1 (Met) to residue number 15 (Ala); (ii) the amino acidsequence of SEQ ID NO:2 from residue number 16 (Arg) to residue number219 (Gln); and at least one other DNA segment encoding an additionalpolypeptide, wherein the first and other DNA segments are connectedin-frame; and encode the fusion protein; and (c) a transcriptionalterminator; and recovering the protein encoded by the DNA segment.
 2. Anisolated polypeptide which consists of a sequence of amino acid residuesselected from the group consisting of: (a) the amino acid sequence asshown in SEQ ID NO: 2 from amino acid number 16 (Arg) to amino acidnumber 37 (Ser); (b) the amino acid sequence as shown in SEQ ID NO: 2from amino acid number 38 (Leu) to amino acid number 126 (Ala); (c) theamino acid sequence as shown in SEQ ID NO: 2 from amino acid number 127(Pro) to amino acid number 219 (Gln); (d) the amino acid sequence asshown in SEQ ID NO:2 from amino acid number 16 (Arg) to amino acidnumber 219 (Gln); and (e) the amino acid sequence as shown in SEQ IDNO:2 from amino acid number 1 (Met) to amino acid number 219 (Gln). 3.An isolated polypeptide according to claim 2, wherein the polypeptideencoded by the polynucleotide has activity as measured by activation oftranscription of a reporter gene, anti-microbial activity, or whereinthe polypeptide encoded by the polynucleotide further binds to anantibody, wherein the antibody is raised to a polypeptide which consistsof a sequence of amino acids selected from the group consisting of: (a)the amino acid sequence as shown in SEQ ID NO: 2 from amino acid number16 (Arg) to amino acid number 37 (Ser); (b) the amino acid sequence asshown in SEQ ID NO: 2 from amino acid number 38 (Leu) to amino acidnumber 126 (Ala); (c) the amino acid sequence as shown in SEQ ID NO: 2from amino acid number 127 (Pro) to amino acid number 219 (Gln); (d) theamino acid sequence as shown in SEQ ID NO:2 from amino acid number 16(Arg) to amino acid number 219 (Gln); and (e) the amino acid sequence asshown in SEQ ID NO:2 from amino acid number 1 (Met) to amino acid number219 (Gln); and wherein the binding of the antibody to the isolatedpolypeptide is measured by a biological or biochemical assay includingradioimmunoassay, radioimmuno-precipitation, Western blot, orenzyme-linked immunosorbent assay.